Magnet hypothesis: plant-pollinator interactions
Purpose: A test of the magnet hypothesis was examined in Mojave National Preserve by Ally Ruttan.
Hypothesis: Floral resource island created by shrubs and the associated beneficiary annual plants will positively and non-additively influence pollinator visitation rates.
Predictions:
(1) The frequency and duration of pollinator visitations to annuals is greater under shrubs than in the paired-open microsites (magnet H because of concentration).
(2) Annual plants under flowering entomophilous shrubs (Larrea tridentata) will have a higher frequency and duration of pollinator visitations than annual plants under anemophilous shrubs (Ambrosia dumosa) because of higher concentrations of suitable floral resources for pollinators (specificity of pollinator faciliation).
(3) Shrubs with annuals in their understory will have a higher frequency and duration of pollinator visitations than shrubs without annuals due to increased concentrations of floral resources for pollinators (reverse magnet effect and reciprocal benefits).
(4) Sites with both shrubs and annuals will have the highest frequency and duration of pollinator visitations to both the shrubs and the annuals (i.e. annuals under shrubs also with flowers are visited the most).
An interesting corollary is that there are appropriate floral resources for desert pollinators, that they discriminate, and that entomophilous and anemophilous shrubs facilitate flowering similarly.
Data wrangling
#libraries####
library(tidyverse)
library(DT)
library(lubridate)
#meta-data####
meta <- read_csv("data/meta-data.csv")
datatable(meta)#error is SD
#data####
data.2015 <- read_csv("data/MNP.2015.csv")
data.2016 <- read_csv("data/MNP.2016.csv")
#merge
data <- rbind.data.frame(data.2015, data.2016)
#code treatment properly
data <- data %>% rename(net.treatment = treatment) #%>% na.omit(data)
#keep key columns and minimize working dataframe
data <- data %>% select(-name, -plant, -start, -stop, -ID, -recorder)
#set year and rep as characters
data$year <- as.character(data$year)
data$rep <- as.character(data$rep)
#convert times to total seconds then to hour
data$total.duration <- (as.numeric(data$total.duration))/3600
data$visitation.duration <- (as.numeric(data$visitation.duration))/3600
#recode net.treatment column
data <- data %>% mutate(net.treatment = ifelse(net.treatment %in% c("SA"), "Larrea flowers with annuals", ifelse(net.treatment %in% c("SX"), "Larrea flowers without annuals", ifelse(net.treatment %in% c("SAA"), "Annual flowers under Larrea",ifelse(net.treatment %in% c("OA"), "Annual flowers in open",ifelse(net.treatment %in% c("AMB"), "Annual flowers under Ambrosia","NA"))))))
#frequency wrangled by RTU####
frequency <- data %>% group_by(year, day, net.treatment, rep, insect.RTU) %>%
summarise(net.time = sum(total.duration), mean.time = mean(total.duration), mean.temp = mean(temperature), mean.var.temp = mean(error), net.visitation = sum(visitation.duration), mean.visitation.duration = mean(visitation.duration), net.floral.density = sum(floral.density), mean.floral.density = mean(floral.density), insect.richness = n_distinct(insect.RTU), count = n())
#richness in RTU
#richness <- frequency %>% group_by(year, day, net.treatment, rep) %>% summarise( insect.richness = mean(insect.richness)) #did not work correctly. need to wrangle data differently
#rates needed
frequency <- frequency %>% mutate(rate.per.flower = (count/mean.floral.density)) %>% mutate(rate.per.flower.hr = rate.per.flower/net.time) %>% mutate(rate.per.flower.mean.time = rate.per.flower/mean.time)
#exclude none and outliers
freq.rtu <- frequency %>% filter(insect.RTU != "none") %>% filter(rate.per.flower.hr <0.4) %>% filter(net.visitation <1) %>% filter(rate.per.flower.mean.time < 2)
frequency <- frequency %>% filter(rate.per.flower.hr <0.4) %>% filter(net.visitation <2)
frequency <- frequency %>% filter(insect.RTU != "none") %>% filter(rate.per.flower.hr <0.4) %>% filter(net.visitation <1) %>% filter(rate.per.flower.mean.time < 2)
#view frequency data
datatable(frequency)#separate by year for stats
freq.2015 <- frequency %>% filter(year == 2015)
freq.2016 <- frequency %>% filter(year == 2016)
#bees only
bees <- frequency %>% filter(insect.RTU == "bees")
bees.2015 <- freq.2015 %>% filter(insect.RTU == "bees")
bees.2016 <- freq.2016 %>% filter(insect.RTU == "bees")
#Single-magnet hypothesis data with bees
magnet.bees.2015 <- bees.2015 %>% filter(net.treatment == "Annual flowers under Larrea" | net.treatment == "Annual flowers in open" | net.treatment == "Annual flowers under Ambrosia")
magnet.bees.2016 <- bees.2016 %>% filter(net.treatment == "Annual flowers under Larrea" | net.treatment == "Annual flowers in open" | net.treatment == "Annual flowers under Ambrosia")
#Double-magnet hypothesis data with bees
double.bees.2015 <- bees.2015 %>% filter(net.treatment == "Larrea flowers with annuals" | net.treatment == "Larrea flowers without annuals")
double.bees.2016 <- bees.2016 %>% filter(net.treatment == "Larrea flowers with annuals" | net.treatment == "Larrea flowers without annuals")Data visualization
#visitations####
ggplot(freq.rtu, aes(net.treatment, count)) + geom_boxplot() + ylab("count") + scale_fill_brewer(palette = "Blues") + facet_wrap(~year) + coord_flip()
ggplot(freq.rtu, aes(net.treatment, count, fill = insect.RTU)) + geom_boxplot() + ylab("count") + scale_fill_brewer(palette = "Blues") + facet_wrap(~year) + coord_flip()
ggplot(freq.rtu, aes(net.treatment, rate.per.flower)) + geom_boxplot() + ylab("rate per flower") + scale_fill_brewer(palette = "Blues") + facet_wrap(~year) + coord_flip()
ggplot(freq.rtu, aes(net.treatment, rate.per.flower, fill = insect.RTU)) + geom_boxplot() + ylab("rate per flower") + scale_fill_brewer(palette = "Blues") + facet_wrap(~year) + coord_flip()
ggplot(freq.rtu, aes(net.treatment, rate.per.flower.mean.time)) + geom_boxplot() + ylab("rate per flower per mean hour recorded time") + scale_fill_brewer(palette = "Blues") + facet_wrap(~year) + coord_flip()
ggplot(freq.rtu, aes(net.treatment, rate.per.flower.mean.time, fill = insect.RTU)) + geom_boxplot() + ylab("rate per flower per mean hour recorded time") + scale_fill_brewer(palette = "Blues") + facet_wrap(~year) + coord_flip()
#visitation durations####
#net visitation time
ggplot(freq.rtu, aes(net.treatment, net.visitation)) + geom_boxplot() + ylab("net duration of visits (proportion of hour)") + scale_fill_brewer(palette = "Blues") + facet_wrap(~year) + coord_flip()
ggplot(freq.rtu, aes(net.treatment, net.visitation, fill = insect.RTU)) + geom_boxplot() + ylab("net duration of visits (proportion of hour)") + scale_fill_brewer(palette = "Blues") + facet_wrap(~year) + coord_flip()
#temperature####
ggplot(freq.rtu, aes(mean.temp, rate.per.flower, color = insect.RTU)) + geom_point() + ylab("rate per flower") + geom_smooth(method = "lm") + facet_wrap(~year)
ggplot(freq.rtu, aes(mean.temp, rate.per.flower.mean.time, color = insect.RTU)) + geom_point() + ylab("rate per flower per mean hour recorded time") + geom_smooth(method = "lm") + facet_wrap(~year)
ggplot(freq.rtu, aes(mean.temp, net.visitation, color = insect.RTU)) + geom_point() + ylab("net duration of visits") + geom_smooth(method = "lm") + facet_wrap(~year)
#floral density####
ggplot(freq.rtu, aes(mean.floral.density, rate.per.flower, color = insect.RTU)) + geom_point() + ylab("rate per flower") + geom_smooth(method = "lm") + facet_wrap(~year)
ggplot(freq.rtu, aes(mean.floral.density, rate.per.flower.mean.time, color = insect.RTU)) + geom_point() + ylab("rate per flower per mean hour recorded time") + geom_smooth(method = "lm") + facet_wrap(~year)
ggplot(freq.rtu, aes(mean.floral.density, net.visitation, color = insect.RTU)) + geom_point() + ylab("net duration of visits") + geom_smooth(method = "lm") + facet_wrap(~year)
EDA
summary(frequency)## year day net.treatment
## Length:491 Length:491 Length:491
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
## rep insect.RTU net.time mean.time
## Length:491 Length:491 Min. : 0.250 Min. :0.2276
## Class :character Class :character 1st Qu.: 0.500 1st Qu.:0.2500
## Mode :character Mode :character Median : 1.825 Median :1.1310
## Mean : 7.591 Mean :0.9273
## 3rd Qu.: 6.759 3rd Qu.:1.3954
## Max. :136.626 Max. :1.6197
## mean.temp mean.var.temp net.visitation
## Min. :11.45 Min. :0.2574 Min. :0.0000000
## 1st Qu.:21.11 1st Qu.:1.0667 1st Qu.:0.0005556
## Median :24.97 Median :1.8703 Median :0.0108333
## Mean :24.37 Mean :2.3842 Mean :0.0771849
## 3rd Qu.:27.65 3rd Qu.:3.0306 3rd Qu.:0.0875000
## Max. :33.97 Max. :6.8652 Max. :0.9463889
## mean.visitation.duration net.floral.density mean.floral.density
## Min. :0.0000000 Min. : 5.0 Min. : 4.00
## 1st Qu.:0.0002778 1st Qu.: 46.5 1st Qu.: 17.00
## Median :0.0048611 Median : 200.0 Median : 31.00
## Mean :0.0108504 Mean : 291.0 Mean : 89.46
## 3rd Qu.:0.0120364 3rd Qu.: 400.0 3rd Qu.:200.00
## Max. :0.1588889 Max. :2821.0 Max. :200.00
## insect.richness count rate.per.flower rate.per.flower.hr
## Min. :1 Min. : 1.000 Min. :0.0050 Min. :0.009245
## 1st Qu.:1 1st Qu.: 1.000 1st Qu.:0.0100 1st Qu.:0.020000
## Median :1 Median : 2.000 Median :0.0625 Median :0.022539
## Mean :1 Mean : 6.363 Mean :0.2860 Mean :0.035339
## 3rd Qu.:1 3rd Qu.: 6.000 3rd Qu.:0.3000 3rd Qu.:0.044222
## Max. :1 Max. :91.000 Max. :2.9355 Max. :0.170648
## rate.per.flower.mean.time
## Min. :0.01849
## 1st Qu.:0.03238
## Median :0.06364
## Mean :0.22851
## 3rd Qu.:0.22148
## Max. :1.95518#distributions
require(fitdistrplus)
descdist(frequency$rate.per.flower, boot = 1000)
## summary statistics
## ------
## min: 0.005 max: 2.935484
## median: 0.0625
## mean: 0.2859648
## estimated sd: 0.4996309
## estimated skewness: 2.543538
## estimated kurtosis: 9.390094descdist(frequency$rate.per.flower.mean.time, boot = 1000)
## summary statistics
## ------
## min: 0.01849022 max: 1.955179
## median: 0.06364123
## mean: 0.2285103
## estimated sd: 0.3770836
## estimated skewness: 2.605647
## estimated kurtosis: 9.506303descdist(frequency$net.visitation, boot = 1000)
## summary statistics
## ------
## min: 0 max: 0.9463889
## median: 0.01083333
## mean: 0.07718488
## estimated sd: 0.1435749
## estimated skewness: 2.841609
## estimated kurtosis: 12.40795#plots
plotdist(frequency$rate.per.flower)
plotdist(frequency$rate.per.flower.mean.time)
plotdist(frequency$net.visitation)
#fitting
a <- frequency$rate.per.flower
fitg <- fitdist(a, "gamma")
fitw <- fitdist(a, "weibull")
fitn <- fitdist(a, "norm")
fitl <- fitdist(a, "lnorm")
gofstat(list(fitg, fitw, fitn, fitl), fitnames = c("gamma", "weibull", "normal", "lognormal"))## Goodness-of-fit statistics
## gamma weibull normal lognormal
## Kolmogorov-Smirnov statistic 0.1339425 0.1288865 0.2867453 0.1143861
## Cramer-von Mises statistic 2.4584535 1.1774767 13.5992885 0.9455949
## Anderson-Darling statistic 14.7869904 8.9084667 70.6985821 7.8267494
##
## Goodness-of-fit criteria
## gamma weibull normal lognormal
## Akaike's Information Criterion -568.3409 -614.1379 715.0009 -669.4631
## Bayesian Information Criterion -559.9480 -605.7450 723.3938 -661.0702a <- frequency$rate.per.flower.mean.time
fitg <- fitdist(a, "gamma")
fitw <- fitdist(a, "weibull")
fitn <- fitdist(a, "norm")
fitl <- fitdist(a, "lnorm")
gofstat(list(fitg, fitw, fitn, fitl), fitnames = c("gamma", "weibull", "normal", "lognormal"))## Goodness-of-fit statistics
## gamma weibull normal lognormal
## Kolmogorov-Smirnov statistic 0.1712137 0.1815332 0.2885837 0.1271809
## Cramer-von Mises statistic 5.1774716 3.3367550 14.4437869 1.8723755
## Anderson-Darling statistic 28.2275221 20.3946910 74.5720226 12.4976228
##
## Goodness-of-fit criteria
## gamma weibull normal lognormal
## Akaike's Information Criterion -534.7070 -580.2532 438.6633 -717.2037
## Bayesian Information Criterion -526.3141 -571.8604 447.0562 -708.8108a <- frequency$net.visitation
fitn <- fitdist(a, "norm")
gofstat(fitn) ## Goodness-of-fit statistics
## 1-mle-norm
## Kolmogorov-Smirnov statistic 0.2952397
## Cramer-von Mises statistic 14.1661667
## Anderson-Darling statistic 71.2237217
##
## Goodness-of-fit criteria
## 1-mle-norm
## Akaike's Information Criterion -509.5657
## Bayesian Information Criterion -501.1728detach("package:fitdistrplus", unload = TRUE)
#summary: gamma, gamma, normal have lowers AIC scoresModel: all with interaction terms
#Interaction-term models for all insect taxa####
#visitations
m <- glm(rate.per.flower~net.treatment:insect.RTU %in% rep + mean.temp, family = "Gamma", data = freq.2015)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: Gamma, link: inverse
##
## Response: rate.per.flower
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 260 585.41
## mean.temp 1 71.35 259 514.06 7.729e-15
## net.treatment:insect.RTU:rep 47 258.76 212 255.31 < 2.2e-16
##
## NULL
## mean.temp ***
## net.treatment:insect.RTU:rep ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1a1 <- AIC(m)
require(lsmeans)
lsmeans(m, pairwise~net.treatment:insect.RTU, adjust="tukey")## $lsmeans
## net.treatment insect.RTU lsmean SE df
## Annual flowers in open bees 5.090819 1.0286834 NA
## Annual flowers under Larrea bees 2.471637 0.6256365 NA
## Larrea flowers with annuals bees 49.035496 11.3380515 NA
## Larrea flowers without annuals bees 23.187193 4.9070882 NA
## Annual flowers in open flies 7.755031 1.3393806 NA
## Annual flowers under Larrea flies 3.449811 1.0255772 NA
## Larrea flowers with annuals flies 64.749381 16.9726820 NA
## Larrea flowers without annuals flies 47.421632 14.6737456 NA
## Annual flowers in open other 8.363670 1.6010934 NA
## Annual flowers under Larrea other 5.894874 1.9618768 NA
## Larrea flowers with annuals other 16.030298 6.7333367 NA
## Larrea flowers without annuals other 13.673377 9.2627934 NA
## asymp.LCL asymp.UCL
## 3.074637 7.107002
## 1.245412 3.697862
## 26.813323 71.257668
## 13.569477 32.804910
## 5.129894 10.380169
## 1.439717 5.459906
## 31.483536 98.015227
## 18.661619 76.181645
## 5.225585 11.501756
## 2.049666 9.740082
## 2.833200 29.227395
## -4.481365 31.828118
##
## Results are averaged over the levels of: rep
## Results are given on the inverse (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast
## Annual flowers in open,bees - Annual flowers under Larrea,bees
## Annual flowers in open,bees - Larrea flowers with annuals,bees
## Annual flowers in open,bees - Larrea flowers without annuals,bees
## Annual flowers in open,bees - Annual flowers in open,flies
## Annual flowers in open,bees - Annual flowers under Larrea,flies
## Annual flowers in open,bees - Larrea flowers with annuals,flies
## Annual flowers in open,bees - Larrea flowers without annuals,flies
## Annual flowers in open,bees - Annual flowers in open,other
## Annual flowers in open,bees - Annual flowers under Larrea,other
## Annual flowers in open,bees - Larrea flowers with annuals,other
## Annual flowers in open,bees - Larrea flowers without annuals,other
## Annual flowers under Larrea,bees - Larrea flowers with annuals,bees
## Annual flowers under Larrea,bees - Larrea flowers without annuals,bees
## Annual flowers under Larrea,bees - Annual flowers in open,flies
## Annual flowers under Larrea,bees - Annual flowers under Larrea,flies
## Annual flowers under Larrea,bees - Larrea flowers with annuals,flies
## Annual flowers under Larrea,bees - Larrea flowers without annuals,flies
## Annual flowers under Larrea,bees - Annual flowers in open,other
## Annual flowers under Larrea,bees - Annual flowers under Larrea,other
## Annual flowers under Larrea,bees - Larrea flowers with annuals,other
## Annual flowers under Larrea,bees - Larrea flowers without annuals,other
## Larrea flowers with annuals,bees - Larrea flowers without annuals,bees
## Larrea flowers with annuals,bees - Annual flowers in open,flies
## Larrea flowers with annuals,bees - Annual flowers under Larrea,flies
## Larrea flowers with annuals,bees - Larrea flowers with annuals,flies
## Larrea flowers with annuals,bees - Larrea flowers without annuals,flies
## Larrea flowers with annuals,bees - Annual flowers in open,other
## Larrea flowers with annuals,bees - Annual flowers under Larrea,other
## Larrea flowers with annuals,bees - Larrea flowers with annuals,other
## Larrea flowers with annuals,bees - Larrea flowers without annuals,other
## Larrea flowers without annuals,bees - Annual flowers in open,flies
## Larrea flowers without annuals,bees - Annual flowers under Larrea,flies
## Larrea flowers without annuals,bees - Larrea flowers with annuals,flies
## Larrea flowers without annuals,bees - Larrea flowers without annuals,flies
## Larrea flowers without annuals,bees - Annual flowers in open,other
## Larrea flowers without annuals,bees - Annual flowers under Larrea,other
## Larrea flowers without annuals,bees - Larrea flowers with annuals,other
## Larrea flowers without annuals,bees - Larrea flowers without annuals,other
## Annual flowers in open,flies - Annual flowers under Larrea,flies
## Annual flowers in open,flies - Larrea flowers with annuals,flies
## Annual flowers in open,flies - Larrea flowers without annuals,flies
## Annual flowers in open,flies - Annual flowers in open,other
## Annual flowers in open,flies - Annual flowers under Larrea,other
## Annual flowers in open,flies - Larrea flowers with annuals,other
## Annual flowers in open,flies - Larrea flowers without annuals,other
## Annual flowers under Larrea,flies - Larrea flowers with annuals,flies
## Annual flowers under Larrea,flies - Larrea flowers without annuals,flies
## Annual flowers under Larrea,flies - Annual flowers in open,other
## Annual flowers under Larrea,flies - Annual flowers under Larrea,other
## Annual flowers under Larrea,flies - Larrea flowers with annuals,other
## Annual flowers under Larrea,flies - Larrea flowers without annuals,other
## Larrea flowers with annuals,flies - Larrea flowers without annuals,flies
## Larrea flowers with annuals,flies - Annual flowers in open,other
## Larrea flowers with annuals,flies - Annual flowers under Larrea,other
## Larrea flowers with annuals,flies - Larrea flowers with annuals,other
## Larrea flowers with annuals,flies - Larrea flowers without annuals,other
## Larrea flowers without annuals,flies - Annual flowers in open,other
## Larrea flowers without annuals,flies - Annual flowers under Larrea,other
## Larrea flowers without annuals,flies - Larrea flowers with annuals,other
## Larrea flowers without annuals,flies - Larrea flowers without annuals,other
## Annual flowers in open,other - Annual flowers under Larrea,other
## Annual flowers in open,other - Larrea flowers with annuals,other
## Annual flowers in open,other - Larrea flowers without annuals,other
## Annual flowers under Larrea,other - Larrea flowers with annuals,other
## Annual flowers under Larrea,other - Larrea flowers without annuals,other
## Larrea flowers with annuals,other - Larrea flowers without annuals,other
## estimate SE df z.ratio p.value
## 2.6191826 1.283453 NA 2.041 0.6653
## -43.9446767 11.412264 NA -3.851 0.0066
## -18.0963741 5.051708 NA -3.582 0.0177
## -2.6642120 1.159231 NA -2.298 0.4777
## 1.6410081 1.526489 NA 1.075 0.9957
## -59.6585619 17.020321 NA -3.505 0.0232
## -42.3308124 14.719506 NA -2.876 0.1495
## -3.2728510 1.399425 NA -2.339 0.4487
## -0.8040545 2.320489 NA -0.347 1.0000
## -10.9394783 6.855599 NA -1.596 0.9111
## -8.5825576 9.353038 NA -0.918 0.9990
## -46.5638593 11.352302 NA -4.102 0.0024
## -20.7155567 4.942638 NA -4.191 0.0017
## -5.2833946 1.532407 NA -3.448 0.0281
## -0.9781745 1.191406 NA -0.821 0.9996
## -62.2777445 16.982424 NA -3.667 0.0131
## -44.9499950 14.686022 NA -3.061 0.0918
## -5.8920336 1.770472 NA -3.328 0.0415
## -3.4232370 2.046657 NA -1.673 0.8809
## -13.5586609 6.757521 NA -2.006 0.6892
## -11.2017402 9.280280 NA -1.207 0.9886
## 25.8483026 12.349063 NA 2.093 0.6278
## 41.2804647 11.439615 NA 3.609 0.0162
## 45.5856848 11.381010 NA 4.005 0.0036
## -15.7138852 20.406618 NA -0.770 0.9998
## 1.6138643 18.541074 NA 0.087 1.0000
## 40.6718257 11.475527 NA 3.544 0.0202
## 43.1406222 11.499388 NA 3.752 0.0096
## 33.0051984 13.178827 NA 2.504 0.3369
## 35.3621191 14.633408 NA 2.417 0.3946
## 15.4321621 5.117458 NA 3.016 0.1039
## 19.7373822 5.008528 NA 3.941 0.0046
## -41.5621878 17.664492 NA -2.353 0.4387
## -24.2344383 15.470567 NA -1.566 0.9211
## 14.8235231 5.195218 NA 2.853 0.1580
## 17.2923197 5.275299 NA 3.278 0.0485
## 7.1568959 8.324145 NA 0.860 0.9994
## 9.5138166 10.476117 NA 0.908 0.9991
## 4.3052201 1.739894 NA 2.474 0.3561
## -56.9943499 17.039028 NA -3.345 0.0393
## -39.6666004 14.742768 NA -2.691 0.2307
## -0.6086390 1.728125 NA -0.352 1.0000
## 1.8601575 2.456931 NA 0.757 0.9998
## -8.2752663 6.901376 NA -1.199 0.9892
## -5.9183456 9.386470 NA -0.631 1.0000
## -61.2995700 17.001653 NA -3.606 0.0163
## -43.9718205 14.708368 NA -2.990 0.1114
## -4.9138591 1.953314 NA -2.516 0.3298
## -2.4450626 2.200753 NA -1.111 0.9943
## -12.5804864 6.805663 NA -1.849 0.7909
## -10.2235657 9.315382 NA -1.097 0.9949
## 17.3277495 22.434410 NA 0.772 0.9998
## 56.3857109 17.062988 NA 3.305 0.0446
## 58.8545074 17.081406 NA 3.446 0.0283
## 48.7190836 18.254445 NA 2.669 0.2418
## 51.0760043 19.330819 NA 2.642 0.2560
## 39.0579614 14.769667 NA 2.644 0.2548
## 41.5267579 14.801787 NA 2.806 0.1774
## 31.3913341 16.141935 NA 1.945 0.7309
## 33.7482548 17.349947 NA 1.945 0.7306
## 2.4687965 2.616585 NA 0.944 0.9987
## -7.6666273 6.960578 NA -1.101 0.9947
## -5.3097066 9.430166 NA -0.563 1.0000
## -10.1354238 7.002097 NA -1.447 0.9540
## -7.7785031 9.459706 NA -0.822 0.9996
## 2.3569207 11.442560 NA 0.206 1.0000
##
## Results are averaged over the levels of: rep
## P value adjustment: tukey method for comparing a family of 12 estimatesm <- glm(rate.per.flower~net.treatment:insect.RTU %in% rep + mean.temp, family = "Gamma", data = freq.2016)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: Gamma, link: inverse
##
## Response: rate.per.flower
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 229 795.36
## mean.temp 1 35.87 228 759.48 < 2.2e-16
## net.treatment:insect.RTU:rep 57 682.21 171 77.28 < 2.2e-16
##
## NULL
## mean.temp ***
## net.treatment:insect.RTU:rep ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1a2 <- AIC(m)
lsmeans(m, pairwise~net.treatment:insect.RTU, adjust="tukey")## $lsmeans
## net.treatment insect.RTU lsmean SE df asymp.LCL
## Annual flowers in open bees 1.908165 0.6590318 NA 0.6164863
## Annual flowers under Ambrosia bees NA NA NA NA
## Annual flowers under Larrea bees NA NA NA NA
## Larrea flowers with annuals bees NA NA NA NA
## Larrea flowers without annuals bees NA NA NA NA
## Annual flowers in open flies NA NA NA NA
## Annual flowers under Ambrosia flies NA NA NA NA
## Annual flowers under Larrea flies NA NA NA NA
## Larrea flowers with annuals flies NA NA NA NA
## Larrea flowers without annuals flies NA NA NA NA
## Annual flowers in open other NA NA NA NA
## Annual flowers under Ambrosia other NA NA NA NA
## Annual flowers under Larrea other NA NA NA NA
## Larrea flowers with annuals other NA NA NA NA
## Larrea flowers without annuals other NA NA NA NA
## asymp.UCL
## 3.199843
## NA
## NA
## NA
## NA
## NA
## NA
## NA
## NA
## NA
## NA
## NA
## NA
## NA
## NA
##
## Results are averaged over the levels of: rep
## Results are given on the inverse (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast
## Annual flowers in open,bees - Annual flowers under Ambrosia,bees
## Annual flowers in open,bees - Annual flowers under Larrea,bees
## Annual flowers in open,bees - Larrea flowers with annuals,bees
## Annual flowers in open,bees - Larrea flowers without annuals,bees
## Annual flowers in open,bees - Annual flowers in open,flies
## Annual flowers in open,bees - Annual flowers under Ambrosia,flies
## Annual flowers in open,bees - Annual flowers under Larrea,flies
## Annual flowers in open,bees - Larrea flowers with annuals,flies
## Annual flowers in open,bees - Larrea flowers without annuals,flies
## Annual flowers in open,bees - Annual flowers in open,other
## Annual flowers in open,bees - Annual flowers under Ambrosia,other
## Annual flowers in open,bees - Annual flowers under Larrea,other
## Annual flowers in open,bees - Larrea flowers with annuals,other
## Annual flowers in open,bees - Larrea flowers without annuals,other
## Annual flowers under Ambrosia,bees - Annual flowers under Larrea,bees
## Annual flowers under Ambrosia,bees - Larrea flowers with annuals,bees
## Annual flowers under Ambrosia,bees - Larrea flowers without annuals,bees
## Annual flowers under Ambrosia,bees - Annual flowers in open,flies
## Annual flowers under Ambrosia,bees - Annual flowers under Ambrosia,flies
## Annual flowers under Ambrosia,bees - Annual flowers under Larrea,flies
## Annual flowers under Ambrosia,bees - Larrea flowers with annuals,flies
## Annual flowers under Ambrosia,bees - Larrea flowers without annuals,flies
## Annual flowers under Ambrosia,bees - Annual flowers in open,other
## Annual flowers under Ambrosia,bees - Annual flowers under Ambrosia,other
## Annual flowers under Ambrosia,bees - Annual flowers under Larrea,other
## Annual flowers under Ambrosia,bees - Larrea flowers with annuals,other
## Annual flowers under Ambrosia,bees - Larrea flowers without annuals,other
## Annual flowers under Larrea,bees - Larrea flowers with annuals,bees
## Annual flowers under Larrea,bees - Larrea flowers without annuals,bees
## Annual flowers under Larrea,bees - Annual flowers in open,flies
## Annual flowers under Larrea,bees - Annual flowers under Ambrosia,flies
## Annual flowers under Larrea,bees - Annual flowers under Larrea,flies
## Annual flowers under Larrea,bees - Larrea flowers with annuals,flies
## Annual flowers under Larrea,bees - Larrea flowers without annuals,flies
## Annual flowers under Larrea,bees - Annual flowers in open,other
## Annual flowers under Larrea,bees - Annual flowers under Ambrosia,other
## Annual flowers under Larrea,bees - Annual flowers under Larrea,other
## Annual flowers under Larrea,bees - Larrea flowers with annuals,other
## Annual flowers under Larrea,bees - Larrea flowers without annuals,other
## Larrea flowers with annuals,bees - Larrea flowers without annuals,bees
## Larrea flowers with annuals,bees - Annual flowers in open,flies
## Larrea flowers with annuals,bees - Annual flowers under Ambrosia,flies
## Larrea flowers with annuals,bees - Annual flowers under Larrea,flies
## Larrea flowers with annuals,bees - Larrea flowers with annuals,flies
## Larrea flowers with annuals,bees - Larrea flowers without annuals,flies
## Larrea flowers with annuals,bees - Annual flowers in open,other
## Larrea flowers with annuals,bees - Annual flowers under Ambrosia,other
## Larrea flowers with annuals,bees - Annual flowers under Larrea,other
## Larrea flowers with annuals,bees - Larrea flowers with annuals,other
## Larrea flowers with annuals,bees - Larrea flowers without annuals,other
## Larrea flowers without annuals,bees - Annual flowers in open,flies
## Larrea flowers without annuals,bees - Annual flowers under Ambrosia,flies
## Larrea flowers without annuals,bees - Annual flowers under Larrea,flies
## Larrea flowers without annuals,bees - Larrea flowers with annuals,flies
## Larrea flowers without annuals,bees - Larrea flowers without annuals,flies
## Larrea flowers without annuals,bees - Annual flowers in open,other
## Larrea flowers without annuals,bees - Annual flowers under Ambrosia,other
## Larrea flowers without annuals,bees - Annual flowers under Larrea,other
## Larrea flowers without annuals,bees - Larrea flowers with annuals,other
## Larrea flowers without annuals,bees - Larrea flowers without annuals,other
## Annual flowers in open,flies - Annual flowers under Ambrosia,flies
## Annual flowers in open,flies - Annual flowers under Larrea,flies
## Annual flowers in open,flies - Larrea flowers with annuals,flies
## Annual flowers in open,flies - Larrea flowers without annuals,flies
## Annual flowers in open,flies - Annual flowers in open,other
## Annual flowers in open,flies - Annual flowers under Ambrosia,other
## Annual flowers in open,flies - Annual flowers under Larrea,other
## Annual flowers in open,flies - Larrea flowers with annuals,other
## Annual flowers in open,flies - Larrea flowers without annuals,other
## Annual flowers under Ambrosia,flies - Annual flowers under Larrea,flies
## Annual flowers under Ambrosia,flies - Larrea flowers with annuals,flies
## Annual flowers under Ambrosia,flies - Larrea flowers without annuals,flies
## Annual flowers under Ambrosia,flies - Annual flowers in open,other
## Annual flowers under Ambrosia,flies - Annual flowers under Ambrosia,other
## Annual flowers under Ambrosia,flies - Annual flowers under Larrea,other
## Annual flowers under Ambrosia,flies - Larrea flowers with annuals,other
## Annual flowers under Ambrosia,flies - Larrea flowers without annuals,other
## Annual flowers under Larrea,flies - Larrea flowers with annuals,flies
## Annual flowers under Larrea,flies - Larrea flowers without annuals,flies
## Annual flowers under Larrea,flies - Annual flowers in open,other
## Annual flowers under Larrea,flies - Annual flowers under Ambrosia,other
## Annual flowers under Larrea,flies - Annual flowers under Larrea,other
## Annual flowers under Larrea,flies - Larrea flowers with annuals,other
## Annual flowers under Larrea,flies - Larrea flowers without annuals,other
## Larrea flowers with annuals,flies - Larrea flowers without annuals,flies
## Larrea flowers with annuals,flies - Annual flowers in open,other
## Larrea flowers with annuals,flies - Annual flowers under Ambrosia,other
## Larrea flowers with annuals,flies - Annual flowers under Larrea,other
## Larrea flowers with annuals,flies - Larrea flowers with annuals,other
## Larrea flowers with annuals,flies - Larrea flowers without annuals,other
## Larrea flowers without annuals,flies - Annual flowers in open,other
## Larrea flowers without annuals,flies - Annual flowers under Ambrosia,other
## Larrea flowers without annuals,flies - Annual flowers under Larrea,other
## Larrea flowers without annuals,flies - Larrea flowers with annuals,other
## Larrea flowers without annuals,flies - Larrea flowers without annuals,other
## Annual flowers in open,other - Annual flowers under Ambrosia,other
## Annual flowers in open,other - Annual flowers under Larrea,other
## Annual flowers in open,other - Larrea flowers with annuals,other
## Annual flowers in open,other - Larrea flowers without annuals,other
## Annual flowers under Ambrosia,other - Annual flowers under Larrea,other
## Annual flowers under Ambrosia,other - Larrea flowers with annuals,other
## Annual flowers under Ambrosia,other - Larrea flowers without annuals,other
## Annual flowers under Larrea,other - Larrea flowers with annuals,other
## Annual flowers under Larrea,other - Larrea flowers without annuals,other
## Larrea flowers with annuals,other - Larrea flowers without annuals,other
## estimate SE df z.ratio p.value
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
##
## Results are averaged over the levels of: rep
## P value adjustment: tukey method for comparing a family of 15 estimatesm <- glm(rate.per.flower.mean.time~net.treatment:insect.RTU %in% rep + mean.temp, family = "Gamma", data = freq.2015)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: Gamma, link: inverse
##
## Response: rate.per.flower.mean.time
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 260 317.65
## mean.temp 1 52.501 259 265.15 < 2.2e-16
## net.treatment:insect.RTU:rep 47 134.866 212 130.28 < 2.2e-16
##
## NULL
## mean.temp ***
## net.treatment:insect.RTU:rep ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1a3 <- AIC(m)
lsmeans(m, pairwise~net.treatment:insect.RTU, adjust="tukey")## $lsmeans
## net.treatment insect.RTU lsmean SE df
## Annual flowers in open bees 6.644304 0.9785245 NA
## Annual flowers under Larrea bees 3.378622 0.6279304 NA
## Larrea flowers with annuals bees 14.120189 2.3722563 NA
## Larrea flowers without annuals bees 19.601627 3.0567939 NA
## Annual flowers in open flies 9.970112 1.2420737 NA
## Annual flowers under Larrea flies 4.787899 1.0259360 NA
## Larrea flowers with annuals flies 29.318600 5.6069502 NA
## Larrea flowers without annuals flies 27.343076 5.2315567 NA
## Annual flowers in open other 11.545209 1.6549062 NA
## Annual flowers under Larrea other 8.325839 1.9803861 NA
## Larrea flowers with annuals other 21.684409 6.8371825 NA
## Larrea flowers without annuals other 21.066784 10.4717261 NA
## asymp.LCL asymp.UCL
## 4.7264314 8.562177
## 2.1479015 4.609343
## 9.4706523 18.769726
## 13.6104209 25.592833
## 7.5356921 12.404531
## 2.7771014 6.798697
## 18.3291800 40.308021
## 17.0894135 37.596739
## 8.3016521 14.788765
## 4.4443541 12.207325
## 8.2837779 35.085041
## 0.5425783 41.590990
##
## Results are averaged over the levels of: rep
## Results are given on the inverse (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast
## Annual flowers in open,bees - Annual flowers under Larrea,bees
## Annual flowers in open,bees - Larrea flowers with annuals,bees
## Annual flowers in open,bees - Larrea flowers without annuals,bees
## Annual flowers in open,bees - Annual flowers in open,flies
## Annual flowers in open,bees - Annual flowers under Larrea,flies
## Annual flowers in open,bees - Larrea flowers with annuals,flies
## Annual flowers in open,bees - Larrea flowers without annuals,flies
## Annual flowers in open,bees - Annual flowers in open,other
## Annual flowers in open,bees - Annual flowers under Larrea,other
## Annual flowers in open,bees - Larrea flowers with annuals,other
## Annual flowers in open,bees - Larrea flowers without annuals,other
## Annual flowers under Larrea,bees - Larrea flowers with annuals,bees
## Annual flowers under Larrea,bees - Larrea flowers without annuals,bees
## Annual flowers under Larrea,bees - Annual flowers in open,flies
## Annual flowers under Larrea,bees - Annual flowers under Larrea,flies
## Annual flowers under Larrea,bees - Larrea flowers with annuals,flies
## Annual flowers under Larrea,bees - Larrea flowers without annuals,flies
## Annual flowers under Larrea,bees - Annual flowers in open,other
## Annual flowers under Larrea,bees - Annual flowers under Larrea,other
## Annual flowers under Larrea,bees - Larrea flowers with annuals,other
## Annual flowers under Larrea,bees - Larrea flowers without annuals,other
## Larrea flowers with annuals,bees - Larrea flowers without annuals,bees
## Larrea flowers with annuals,bees - Annual flowers in open,flies
## Larrea flowers with annuals,bees - Annual flowers under Larrea,flies
## Larrea flowers with annuals,bees - Larrea flowers with annuals,flies
## Larrea flowers with annuals,bees - Larrea flowers without annuals,flies
## Larrea flowers with annuals,bees - Annual flowers in open,other
## Larrea flowers with annuals,bees - Annual flowers under Larrea,other
## Larrea flowers with annuals,bees - Larrea flowers with annuals,other
## Larrea flowers with annuals,bees - Larrea flowers without annuals,other
## Larrea flowers without annuals,bees - Annual flowers in open,flies
## Larrea flowers without annuals,bees - Annual flowers under Larrea,flies
## Larrea flowers without annuals,bees - Larrea flowers with annuals,flies
## Larrea flowers without annuals,bees - Larrea flowers without annuals,flies
## Larrea flowers without annuals,bees - Annual flowers in open,other
## Larrea flowers without annuals,bees - Annual flowers under Larrea,other
## Larrea flowers without annuals,bees - Larrea flowers with annuals,other
## Larrea flowers without annuals,bees - Larrea flowers without annuals,other
## Annual flowers in open,flies - Annual flowers under Larrea,flies
## Annual flowers in open,flies - Larrea flowers with annuals,flies
## Annual flowers in open,flies - Larrea flowers without annuals,flies
## Annual flowers in open,flies - Annual flowers in open,other
## Annual flowers in open,flies - Annual flowers under Larrea,other
## Annual flowers in open,flies - Larrea flowers with annuals,other
## Annual flowers in open,flies - Larrea flowers without annuals,other
## Annual flowers under Larrea,flies - Larrea flowers with annuals,flies
## Annual flowers under Larrea,flies - Larrea flowers without annuals,flies
## Annual flowers under Larrea,flies - Annual flowers in open,other
## Annual flowers under Larrea,flies - Annual flowers under Larrea,other
## Annual flowers under Larrea,flies - Larrea flowers with annuals,other
## Annual flowers under Larrea,flies - Larrea flowers without annuals,other
## Larrea flowers with annuals,flies - Larrea flowers without annuals,flies
## Larrea flowers with annuals,flies - Annual flowers in open,other
## Larrea flowers with annuals,flies - Annual flowers under Larrea,other
## Larrea flowers with annuals,flies - Larrea flowers with annuals,other
## Larrea flowers with annuals,flies - Larrea flowers without annuals,other
## Larrea flowers without annuals,flies - Annual flowers in open,other
## Larrea flowers without annuals,flies - Annual flowers under Larrea,other
## Larrea flowers without annuals,flies - Larrea flowers with annuals,other
## Larrea flowers without annuals,flies - Larrea flowers without annuals,other
## Annual flowers in open,other - Annual flowers under Larrea,other
## Annual flowers in open,other - Larrea flowers with annuals,other
## Annual flowers in open,other - Larrea flowers without annuals,other
## Annual flowers under Larrea,other - Larrea flowers with annuals,other
## Annual flowers under Larrea,other - Larrea flowers without annuals,other
## Larrea flowers with annuals,other - Larrea flowers without annuals,other
## estimate SE df z.ratio p.value
## 3.2656818 1.240374 NA 2.633 0.2611
## -7.4758849 2.660198 NA -2.810 0.1754
## -12.9573227 3.250963 NA -3.986 0.0039
## -3.3258075 1.074098 NA -3.096 0.0831
## 1.8564052 1.489954 NA 1.246 0.9852
## -22.6742962 5.733501 NA -3.955 0.0044
## -20.6987718 5.338150 NA -3.878 0.0059
## -4.9009044 1.487484 NA -3.295 0.0460
## -1.6815352 2.306962 NA -0.729 0.9999
## -15.0401051 6.946200 NA -2.165 0.5752
## -14.4224800 10.543907 NA -1.368 0.9695
## -10.7415668 2.442457 NA -4.398 0.0007
## -16.2230045 3.115714 NA -5.207 <.0001
## -6.5914894 1.446123 NA -4.558 0.0003
## -1.4092766 1.192812 NA -1.181 0.9904
## -25.9399780 5.637152 NA -4.602 0.0003
## -23.9644537 5.267268 NA -4.550 0.0003
## -8.1665862 1.817398 NA -4.494 0.0004
## -4.9472170 2.065316 NA -2.395 0.4090
## -18.3057870 6.861408 NA -2.668 0.2423
## -17.6881618 10.487482 NA -1.687 0.8748
## -5.4814377 3.858887 NA -1.420 0.9598
## 4.1500774 2.752518 NA 1.508 0.9389
## 9.3322901 2.572325 NA 3.628 0.0151
## -15.1984113 6.076304 NA -2.501 0.3389
## -13.2228869 5.739842 NA -2.304 0.4738
## 2.5749805 2.968779 NA 0.867 0.9994
## 5.7943497 3.068561 NA 1.888 0.7669
## -7.5642202 7.225670 NA -1.047 0.9966
## -6.9465951 10.729211 NA -0.647 1.0000
## 9.6315151 3.332790 NA 2.890 0.1443
## 14.8137278 3.219025 NA 4.602 0.0003
## -9.7169735 6.379935 NA -1.523 0.9346
## -7.7414492 6.056851 NA -1.278 0.9819
## 8.0564183 3.510830 NA 2.295 0.4803
## 11.2757875 3.632266 NA 3.104 0.0812
## -2.0827825 7.483427 NA -0.278 1.0000
## -1.4651573 10.904555 NA -0.134 1.0000
## 5.1822127 1.663933 NA 3.114 0.0789
## -19.3484887 5.777124 NA -3.349 0.0388
## -17.3729643 5.389958 NA -3.223 0.0573
## -1.5750969 1.748145 NA -0.901 0.9991
## 1.6442723 2.414598 NA 0.681 0.9999
## -11.7142976 6.981409 NA -1.678 0.8786
## -11.0966725 10.567018 NA -1.050 0.9965
## -24.5307014 5.694641 NA -4.308 0.0010
## -22.5551770 5.329160 NA -4.232 0.0014
## -6.7573096 1.995566 NA -3.386 0.0344
## -3.5379404 2.217540 NA -1.595 0.9112
## -16.8965103 6.908648 NA -2.446 0.3750
## -16.2788852 10.518439 NA -1.548 0.9272
## 1.9755244 7.665345 NA 0.258 1.0000
## 17.7733918 5.883135 NA 3.021 0.1024
## 20.9927610 5.935498 NA 3.537 0.0208
## 7.6341911 8.833190 NA 0.864 0.9994
## 8.2518162 11.871438 NA 0.695 0.9999
## 15.7978674 5.501075 NA 2.872 0.1510
## 19.0172367 5.589740 NA 3.402 0.0327
## 5.6586667 8.605794 NA 0.658 1.0000
## 6.2762918 11.703341 NA 0.536 1.0000
## 3.2193692 2.657718 NA 1.211 0.9882
## -10.1392007 7.069786 NA -1.434 0.9569
## -9.5215756 10.625670 NA -0.896 0.9992
## -13.3585700 7.107812 NA -1.879 0.7723
## -12.7409448 10.650215 NA -1.196 0.9894
## 0.6176251 12.498682 NA 0.049 1.0000
##
## Results are averaged over the levels of: rep
## P value adjustment: tukey method for comparing a family of 12 estimatesm <- glm(rate.per.flower.mean.time~net.treatment:insect.RTU %in% rep + mean.temp, family = "Gamma", data = freq.2016)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: Gamma, link: inverse
##
## Response: rate.per.flower.mean.time
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 229 522.69
## mean.temp 1 38.73 228 483.96 < 2.2e-16
## net.treatment:insect.RTU:rep 57 407.45 171 76.51 < 2.2e-16
##
## NULL
## mean.temp ***
## net.treatment:insect.RTU:rep ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1a4 <- AIC(m)
lsmeans(m, pairwise~net.treatment:insect.RTU, adjust="tukey")## $lsmeans
## net.treatment insect.RTU lsmean SE df asymp.LCL
## Annual flowers in open bees 2.729235 0.9224828 NA 0.921202
## Annual flowers under Ambrosia bees NA NA NA NA
## Annual flowers under Larrea bees NA NA NA NA
## Larrea flowers with annuals bees NA NA NA NA
## Larrea flowers without annuals bees NA NA NA NA
## Annual flowers in open flies NA NA NA NA
## Annual flowers under Ambrosia flies NA NA NA NA
## Annual flowers under Larrea flies NA NA NA NA
## Larrea flowers with annuals flies NA NA NA NA
## Larrea flowers without annuals flies NA NA NA NA
## Annual flowers in open other NA NA NA NA
## Annual flowers under Ambrosia other NA NA NA NA
## Annual flowers under Larrea other NA NA NA NA
## Larrea flowers with annuals other NA NA NA NA
## Larrea flowers without annuals other NA NA NA NA
## asymp.UCL
## 4.537268
## NA
## NA
## NA
## NA
## NA
## NA
## NA
## NA
## NA
## NA
## NA
## NA
## NA
## NA
##
## Results are averaged over the levels of: rep
## Results are given on the inverse (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast
## Annual flowers in open,bees - Annual flowers under Ambrosia,bees
## Annual flowers in open,bees - Annual flowers under Larrea,bees
## Annual flowers in open,bees - Larrea flowers with annuals,bees
## Annual flowers in open,bees - Larrea flowers without annuals,bees
## Annual flowers in open,bees - Annual flowers in open,flies
## Annual flowers in open,bees - Annual flowers under Ambrosia,flies
## Annual flowers in open,bees - Annual flowers under Larrea,flies
## Annual flowers in open,bees - Larrea flowers with annuals,flies
## Annual flowers in open,bees - Larrea flowers without annuals,flies
## Annual flowers in open,bees - Annual flowers in open,other
## Annual flowers in open,bees - Annual flowers under Ambrosia,other
## Annual flowers in open,bees - Annual flowers under Larrea,other
## Annual flowers in open,bees - Larrea flowers with annuals,other
## Annual flowers in open,bees - Larrea flowers without annuals,other
## Annual flowers under Ambrosia,bees - Annual flowers under Larrea,bees
## Annual flowers under Ambrosia,bees - Larrea flowers with annuals,bees
## Annual flowers under Ambrosia,bees - Larrea flowers without annuals,bees
## Annual flowers under Ambrosia,bees - Annual flowers in open,flies
## Annual flowers under Ambrosia,bees - Annual flowers under Ambrosia,flies
## Annual flowers under Ambrosia,bees - Annual flowers under Larrea,flies
## Annual flowers under Ambrosia,bees - Larrea flowers with annuals,flies
## Annual flowers under Ambrosia,bees - Larrea flowers without annuals,flies
## Annual flowers under Ambrosia,bees - Annual flowers in open,other
## Annual flowers under Ambrosia,bees - Annual flowers under Ambrosia,other
## Annual flowers under Ambrosia,bees - Annual flowers under Larrea,other
## Annual flowers under Ambrosia,bees - Larrea flowers with annuals,other
## Annual flowers under Ambrosia,bees - Larrea flowers without annuals,other
## Annual flowers under Larrea,bees - Larrea flowers with annuals,bees
## Annual flowers under Larrea,bees - Larrea flowers without annuals,bees
## Annual flowers under Larrea,bees - Annual flowers in open,flies
## Annual flowers under Larrea,bees - Annual flowers under Ambrosia,flies
## Annual flowers under Larrea,bees - Annual flowers under Larrea,flies
## Annual flowers under Larrea,bees - Larrea flowers with annuals,flies
## Annual flowers under Larrea,bees - Larrea flowers without annuals,flies
## Annual flowers under Larrea,bees - Annual flowers in open,other
## Annual flowers under Larrea,bees - Annual flowers under Ambrosia,other
## Annual flowers under Larrea,bees - Annual flowers under Larrea,other
## Annual flowers under Larrea,bees - Larrea flowers with annuals,other
## Annual flowers under Larrea,bees - Larrea flowers without annuals,other
## Larrea flowers with annuals,bees - Larrea flowers without annuals,bees
## Larrea flowers with annuals,bees - Annual flowers in open,flies
## Larrea flowers with annuals,bees - Annual flowers under Ambrosia,flies
## Larrea flowers with annuals,bees - Annual flowers under Larrea,flies
## Larrea flowers with annuals,bees - Larrea flowers with annuals,flies
## Larrea flowers with annuals,bees - Larrea flowers without annuals,flies
## Larrea flowers with annuals,bees - Annual flowers in open,other
## Larrea flowers with annuals,bees - Annual flowers under Ambrosia,other
## Larrea flowers with annuals,bees - Annual flowers under Larrea,other
## Larrea flowers with annuals,bees - Larrea flowers with annuals,other
## Larrea flowers with annuals,bees - Larrea flowers without annuals,other
## Larrea flowers without annuals,bees - Annual flowers in open,flies
## Larrea flowers without annuals,bees - Annual flowers under Ambrosia,flies
## Larrea flowers without annuals,bees - Annual flowers under Larrea,flies
## Larrea flowers without annuals,bees - Larrea flowers with annuals,flies
## Larrea flowers without annuals,bees - Larrea flowers without annuals,flies
## Larrea flowers without annuals,bees - Annual flowers in open,other
## Larrea flowers without annuals,bees - Annual flowers under Ambrosia,other
## Larrea flowers without annuals,bees - Annual flowers under Larrea,other
## Larrea flowers without annuals,bees - Larrea flowers with annuals,other
## Larrea flowers without annuals,bees - Larrea flowers without annuals,other
## Annual flowers in open,flies - Annual flowers under Ambrosia,flies
## Annual flowers in open,flies - Annual flowers under Larrea,flies
## Annual flowers in open,flies - Larrea flowers with annuals,flies
## Annual flowers in open,flies - Larrea flowers without annuals,flies
## Annual flowers in open,flies - Annual flowers in open,other
## Annual flowers in open,flies - Annual flowers under Ambrosia,other
## Annual flowers in open,flies - Annual flowers under Larrea,other
## Annual flowers in open,flies - Larrea flowers with annuals,other
## Annual flowers in open,flies - Larrea flowers without annuals,other
## Annual flowers under Ambrosia,flies - Annual flowers under Larrea,flies
## Annual flowers under Ambrosia,flies - Larrea flowers with annuals,flies
## Annual flowers under Ambrosia,flies - Larrea flowers without annuals,flies
## Annual flowers under Ambrosia,flies - Annual flowers in open,other
## Annual flowers under Ambrosia,flies - Annual flowers under Ambrosia,other
## Annual flowers under Ambrosia,flies - Annual flowers under Larrea,other
## Annual flowers under Ambrosia,flies - Larrea flowers with annuals,other
## Annual flowers under Ambrosia,flies - Larrea flowers without annuals,other
## Annual flowers under Larrea,flies - Larrea flowers with annuals,flies
## Annual flowers under Larrea,flies - Larrea flowers without annuals,flies
## Annual flowers under Larrea,flies - Annual flowers in open,other
## Annual flowers under Larrea,flies - Annual flowers under Ambrosia,other
## Annual flowers under Larrea,flies - Annual flowers under Larrea,other
## Annual flowers under Larrea,flies - Larrea flowers with annuals,other
## Annual flowers under Larrea,flies - Larrea flowers without annuals,other
## Larrea flowers with annuals,flies - Larrea flowers without annuals,flies
## Larrea flowers with annuals,flies - Annual flowers in open,other
## Larrea flowers with annuals,flies - Annual flowers under Ambrosia,other
## Larrea flowers with annuals,flies - Annual flowers under Larrea,other
## Larrea flowers with annuals,flies - Larrea flowers with annuals,other
## Larrea flowers with annuals,flies - Larrea flowers without annuals,other
## Larrea flowers without annuals,flies - Annual flowers in open,other
## Larrea flowers without annuals,flies - Annual flowers under Ambrosia,other
## Larrea flowers without annuals,flies - Annual flowers under Larrea,other
## Larrea flowers without annuals,flies - Larrea flowers with annuals,other
## Larrea flowers without annuals,flies - Larrea flowers without annuals,other
## Annual flowers in open,other - Annual flowers under Ambrosia,other
## Annual flowers in open,other - Annual flowers under Larrea,other
## Annual flowers in open,other - Larrea flowers with annuals,other
## Annual flowers in open,other - Larrea flowers without annuals,other
## Annual flowers under Ambrosia,other - Annual flowers under Larrea,other
## Annual flowers under Ambrosia,other - Larrea flowers with annuals,other
## Annual flowers under Ambrosia,other - Larrea flowers without annuals,other
## Annual flowers under Larrea,other - Larrea flowers with annuals,other
## Annual flowers under Larrea,other - Larrea flowers without annuals,other
## Larrea flowers with annuals,other - Larrea flowers without annuals,other
## estimate SE df z.ratio p.value
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
##
## Results are averaged over the levels of: rep
## P value adjustment: tukey method for comparing a family of 15 estimates#duration of visits
m <- glm(net.visitation~net.treatment:insect.RTU %in% rep + mean.temp, family = "gaussian", data = freq.2015)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: gaussian, link: identity
##
## Response: net.visitation
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 260 4.1594
## mean.temp 1 0.20825 259 3.9511 4.324e-05
## net.treatment:insect.RTU:rep 47 1.31116 212 2.6400 2.346e-06
##
## NULL
## mean.temp ***
## net.treatment:insect.RTU:rep ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1a5 <- AIC(m)
lsmeans(m, pairwise~net.treatment:insect.RTU, adjust="tukey")## $lsmeans
## net.treatment insect.RTU lsmean SE df
## Annual flowers in open bees 0.158604874 0.02455790 NA
## Annual flowers under Larrea bees 0.141744757 0.02097419 NA
## Larrea flowers with annuals bees 0.012555229 0.02163731 NA
## Larrea flowers without annuals bees 0.012545125 0.02116279 NA
## Annual flowers in open flies 0.090058567 0.02456167 NA
## Annual flowers under Larrea flies 0.101023055 0.02625699 NA
## Larrea flowers with annuals flies 0.011592533 0.02615924 NA
## Larrea flowers without annuals flies 0.006948023 0.02541023 NA
## Annual flowers in open other -0.004183146 0.02905800 NA
## Annual flowers under Larrea other 0.077733225 0.02842443 NA
## Larrea flowers with annuals other 0.019406684 0.04159875 NA
## Larrea flowers without annuals other 0.032689106 0.05272290 NA
## asymp.LCL asymp.UCL
## 0.11047227 0.20673748
## 0.10063609 0.18285342
## -0.02985312 0.05496358
## -0.02893319 0.05402344
## 0.04191859 0.13819855
## 0.04956031 0.15248580
## -0.03967864 0.06286371
## -0.04285512 0.05675116
## -0.06113577 0.05276948
## 0.02202237 0.13344408
## -0.06212536 0.10093873
## -0.07064588 0.13602410
##
## Results are averaged over the levels of: rep
## Results are given on the identity (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast
## Annual flowers in open,bees - Annual flowers under Larrea,bees
## Annual flowers in open,bees - Larrea flowers with annuals,bees
## Annual flowers in open,bees - Larrea flowers without annuals,bees
## Annual flowers in open,bees - Annual flowers in open,flies
## Annual flowers in open,bees - Annual flowers under Larrea,flies
## Annual flowers in open,bees - Larrea flowers with annuals,flies
## Annual flowers in open,bees - Larrea flowers without annuals,flies
## Annual flowers in open,bees - Annual flowers in open,other
## Annual flowers in open,bees - Annual flowers under Larrea,other
## Annual flowers in open,bees - Larrea flowers with annuals,other
## Annual flowers in open,bees - Larrea flowers without annuals,other
## Annual flowers under Larrea,bees - Larrea flowers with annuals,bees
## Annual flowers under Larrea,bees - Larrea flowers without annuals,bees
## Annual flowers under Larrea,bees - Annual flowers in open,flies
## Annual flowers under Larrea,bees - Annual flowers under Larrea,flies
## Annual flowers under Larrea,bees - Larrea flowers with annuals,flies
## Annual flowers under Larrea,bees - Larrea flowers without annuals,flies
## Annual flowers under Larrea,bees - Annual flowers in open,other
## Annual flowers under Larrea,bees - Annual flowers under Larrea,other
## Annual flowers under Larrea,bees - Larrea flowers with annuals,other
## Annual flowers under Larrea,bees - Larrea flowers without annuals,other
## Larrea flowers with annuals,bees - Larrea flowers without annuals,bees
## Larrea flowers with annuals,bees - Annual flowers in open,flies
## Larrea flowers with annuals,bees - Annual flowers under Larrea,flies
## Larrea flowers with annuals,bees - Larrea flowers with annuals,flies
## Larrea flowers with annuals,bees - Larrea flowers without annuals,flies
## Larrea flowers with annuals,bees - Annual flowers in open,other
## Larrea flowers with annuals,bees - Annual flowers under Larrea,other
## Larrea flowers with annuals,bees - Larrea flowers with annuals,other
## Larrea flowers with annuals,bees - Larrea flowers without annuals,other
## Larrea flowers without annuals,bees - Annual flowers in open,flies
## Larrea flowers without annuals,bees - Annual flowers under Larrea,flies
## Larrea flowers without annuals,bees - Larrea flowers with annuals,flies
## Larrea flowers without annuals,bees - Larrea flowers without annuals,flies
## Larrea flowers without annuals,bees - Annual flowers in open,other
## Larrea flowers without annuals,bees - Annual flowers under Larrea,other
## Larrea flowers without annuals,bees - Larrea flowers with annuals,other
## Larrea flowers without annuals,bees - Larrea flowers without annuals,other
## Annual flowers in open,flies - Annual flowers under Larrea,flies
## Annual flowers in open,flies - Larrea flowers with annuals,flies
## Annual flowers in open,flies - Larrea flowers without annuals,flies
## Annual flowers in open,flies - Annual flowers in open,other
## Annual flowers in open,flies - Annual flowers under Larrea,other
## Annual flowers in open,flies - Larrea flowers with annuals,other
## Annual flowers in open,flies - Larrea flowers without annuals,other
## Annual flowers under Larrea,flies - Larrea flowers with annuals,flies
## Annual flowers under Larrea,flies - Larrea flowers without annuals,flies
## Annual flowers under Larrea,flies - Annual flowers in open,other
## Annual flowers under Larrea,flies - Annual flowers under Larrea,other
## Annual flowers under Larrea,flies - Larrea flowers with annuals,other
## Annual flowers under Larrea,flies - Larrea flowers without annuals,other
## Larrea flowers with annuals,flies - Larrea flowers without annuals,flies
## Larrea flowers with annuals,flies - Annual flowers in open,other
## Larrea flowers with annuals,flies - Annual flowers under Larrea,other
## Larrea flowers with annuals,flies - Larrea flowers with annuals,other
## Larrea flowers with annuals,flies - Larrea flowers without annuals,other
## Larrea flowers without annuals,flies - Annual flowers in open,other
## Larrea flowers without annuals,flies - Annual flowers under Larrea,other
## Larrea flowers without annuals,flies - Larrea flowers with annuals,other
## Larrea flowers without annuals,flies - Larrea flowers without annuals,other
## Annual flowers in open,other - Annual flowers under Larrea,other
## Annual flowers in open,other - Larrea flowers with annuals,other
## Annual flowers in open,other - Larrea flowers without annuals,other
## Annual flowers under Larrea,other - Larrea flowers with annuals,other
## Annual flowers under Larrea,other - Larrea flowers without annuals,other
## Larrea flowers with annuals,other - Larrea flowers without annuals,other
## estimate SE df z.ratio p.value
## 1.686012e-02 0.03467556 NA 0.486 1.0000
## 1.460496e-01 0.03536159 NA 4.130 0.0021
## 1.460597e-01 0.03459643 NA 4.222 0.0015
## 6.854631e-02 0.02959503 NA 2.316 0.4648
## 5.758182e-02 0.03733451 NA 1.542 0.9288
## 1.470123e-01 0.03800382 NA 3.868 0.0062
## 1.516569e-01 0.03677703 NA 4.124 0.0022
## 1.627880e-01 0.03243035 NA 5.020 <.0001
## 8.087165e-02 0.03977952 NA 2.033 0.6707
## 1.391982e-01 0.05007951 NA 2.780 0.1886
## 1.259158e-01 0.05982180 NA 2.105 0.6193
## 1.291895e-01 0.02872613 NA 4.497 0.0004
## 1.291996e-01 0.02864002 NA 4.511 0.0004
## 5.168619e-02 0.03458472 NA 1.494 0.9425
## 4.072170e-02 0.03290071 NA 1.238 0.9860
## 1.301522e-01 0.03242890 NA 4.013 0.0035
## 1.347967e-01 0.03221151 NA 4.185 0.0017
## 1.459279e-01 0.03830632 NA 3.809 0.0077
## 6.401153e-02 0.03418446 NA 1.873 0.7765
## 1.223381e-01 0.04571300 NA 2.676 0.2380
## 1.090557e-01 0.05593753 NA 1.950 0.7276
## 1.010307e-05 0.02898485 NA 0.000 1.0000
## -7.750334e-02 0.03526112 NA -2.198 0.5511
## -8.846783e-02 0.03323990 NA -2.661 0.2457
## 9.626951e-04 0.03272424 NA 0.029 1.0000
## 5.607206e-03 0.03255573 NA 0.172 1.0000
## 1.673837e-02 0.03896621 NA 0.430 1.0000
## -6.517800e-02 0.03445269 NA -1.892 0.7647
## -6.851456e-03 0.04591203 NA -0.149 1.0000
## -2.013388e-02 0.05608932 NA -0.359 1.0000
## -7.751344e-02 0.03451329 NA -2.246 0.5159
## -8.847793e-02 0.03308103 NA -2.675 0.2389
## 9.525920e-04 0.03264500 NA 0.029 1.0000
## 5.597103e-03 0.03239713 NA 0.173 1.0000
## 1.672827e-02 0.03820859 NA 0.438 1.0000
## -6.518810e-02 0.03439774 NA -1.895 0.7626
## -6.861559e-03 0.04587400 NA -0.150 1.0000
## -2.014398e-02 0.05607663 NA -0.359 1.0000
## -1.096449e-02 0.03728180 NA -0.294 1.0000
## 7.846603e-02 0.03792230 NA 2.069 0.6451
## 8.311054e-02 0.03672218 NA 2.263 0.5032
## 9.424171e-02 0.03268015 NA 2.884 0.1465
## 1.232534e-02 0.03969423 NA 0.311 1.0000
## 7.065188e-02 0.05001056 NA 1.413 0.9614
## 5.736946e-02 0.05975680 NA 0.960 0.9984
## 8.943052e-02 0.03643596 NA 2.454 0.3692
## 9.407503e-02 0.03611895 NA 2.605 0.2768
## 1.052062e-01 0.04062283 NA 2.590 0.2853
## 2.328983e-02 0.03803896 NA 0.612 1.0000
## 8.161637e-02 0.04866802 NA 1.677 0.8790
## 6.833395e-02 0.05840819 NA 1.170 0.9912
## 4.644511e-03 0.03581510 NA 0.130 1.0000
## 1.577568e-02 0.04133884 NA 0.382 1.0000
## -6.614069e-02 0.03760594 NA -1.759 0.8403
## -7.814151e-03 0.04832525 NA -0.162 1.0000
## -2.109657e-02 0.05809315 NA -0.363 1.0000
## 1.113117e-02 0.04011559 NA 0.277 1.0000
## -7.078520e-02 0.03744332 NA -1.890 0.7655
## -1.245866e-02 0.04820367 NA -0.258 1.0000
## -2.574108e-02 0.05802055 NA -0.444 1.0000
## -8.191637e-02 0.04300201 NA -1.905 0.7565
## -2.358983e-02 0.05267990 NA -0.448 1.0000
## -3.687225e-02 0.06204072 NA -0.594 1.0000
## 5.832654e-02 0.04951406 NA 1.178 0.9906
## 4.504412e-02 0.05907812 NA 0.762 0.9998
## -1.328242e-02 0.06641539 NA -0.200 1.0000
##
## Results are averaged over the levels of: rep
## P value adjustment: tukey method for comparing a family of 12 estimatesm <- glm(net.visitation~net.treatment:insect.RTU %in% rep, family = "gaussian", data = freq.2016)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: gaussian, link: identity
##
## Response: net.visitation
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 229 5.8264
## net.treatment:insect.RTU:rep 57 3.7091 172 2.1173 < 2.2e-16
##
## NULL
## net.treatment:insect.RTU:rep ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1a6 <- AIC(m)
lsmeans(m, pairwise~net.treatment:insect.RTU, adjust="tukey")## $lsmeans
## net.treatment insect.RTU lsmean SE df
## Annual flowers in open bees 0.2015817 0.02852403 NA
## Annual flowers under Ambrosia bees NA NA NA
## Annual flowers under Larrea bees NA NA NA
## Larrea flowers with annuals bees NA NA NA
## Larrea flowers without annuals bees NA NA NA
## Annual flowers in open flies NA NA NA
## Annual flowers under Ambrosia flies NA NA NA
## Annual flowers under Larrea flies NA NA NA
## Larrea flowers with annuals flies NA NA NA
## Larrea flowers without annuals flies NA NA NA
## Annual flowers in open other NA NA NA
## Annual flowers under Ambrosia other NA NA NA
## Annual flowers under Larrea other NA NA NA
## Larrea flowers with annuals other NA NA NA
## Larrea flowers without annuals other NA NA NA
## asymp.LCL asymp.UCL
## 0.1456757 0.2574878
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
##
## Results are averaged over the levels of: rep
## Results are given on the identity (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast
## Annual flowers in open,bees - Annual flowers under Ambrosia,bees
## Annual flowers in open,bees - Annual flowers under Larrea,bees
## Annual flowers in open,bees - Larrea flowers with annuals,bees
## Annual flowers in open,bees - Larrea flowers without annuals,bees
## Annual flowers in open,bees - Annual flowers in open,flies
## Annual flowers in open,bees - Annual flowers under Ambrosia,flies
## Annual flowers in open,bees - Annual flowers under Larrea,flies
## Annual flowers in open,bees - Larrea flowers with annuals,flies
## Annual flowers in open,bees - Larrea flowers without annuals,flies
## Annual flowers in open,bees - Annual flowers in open,other
## Annual flowers in open,bees - Annual flowers under Ambrosia,other
## Annual flowers in open,bees - Annual flowers under Larrea,other
## Annual flowers in open,bees - Larrea flowers with annuals,other
## Annual flowers in open,bees - Larrea flowers without annuals,other
## Annual flowers under Ambrosia,bees - Annual flowers under Larrea,bees
## Annual flowers under Ambrosia,bees - Larrea flowers with annuals,bees
## Annual flowers under Ambrosia,bees - Larrea flowers without annuals,bees
## Annual flowers under Ambrosia,bees - Annual flowers in open,flies
## Annual flowers under Ambrosia,bees - Annual flowers under Ambrosia,flies
## Annual flowers under Ambrosia,bees - Annual flowers under Larrea,flies
## Annual flowers under Ambrosia,bees - Larrea flowers with annuals,flies
## Annual flowers under Ambrosia,bees - Larrea flowers without annuals,flies
## Annual flowers under Ambrosia,bees - Annual flowers in open,other
## Annual flowers under Ambrosia,bees - Annual flowers under Ambrosia,other
## Annual flowers under Ambrosia,bees - Annual flowers under Larrea,other
## Annual flowers under Ambrosia,bees - Larrea flowers with annuals,other
## Annual flowers under Ambrosia,bees - Larrea flowers without annuals,other
## Annual flowers under Larrea,bees - Larrea flowers with annuals,bees
## Annual flowers under Larrea,bees - Larrea flowers without annuals,bees
## Annual flowers under Larrea,bees - Annual flowers in open,flies
## Annual flowers under Larrea,bees - Annual flowers under Ambrosia,flies
## Annual flowers under Larrea,bees - Annual flowers under Larrea,flies
## Annual flowers under Larrea,bees - Larrea flowers with annuals,flies
## Annual flowers under Larrea,bees - Larrea flowers without annuals,flies
## Annual flowers under Larrea,bees - Annual flowers in open,other
## Annual flowers under Larrea,bees - Annual flowers under Ambrosia,other
## Annual flowers under Larrea,bees - Annual flowers under Larrea,other
## Annual flowers under Larrea,bees - Larrea flowers with annuals,other
## Annual flowers under Larrea,bees - Larrea flowers without annuals,other
## Larrea flowers with annuals,bees - Larrea flowers without annuals,bees
## Larrea flowers with annuals,bees - Annual flowers in open,flies
## Larrea flowers with annuals,bees - Annual flowers under Ambrosia,flies
## Larrea flowers with annuals,bees - Annual flowers under Larrea,flies
## Larrea flowers with annuals,bees - Larrea flowers with annuals,flies
## Larrea flowers with annuals,bees - Larrea flowers without annuals,flies
## Larrea flowers with annuals,bees - Annual flowers in open,other
## Larrea flowers with annuals,bees - Annual flowers under Ambrosia,other
## Larrea flowers with annuals,bees - Annual flowers under Larrea,other
## Larrea flowers with annuals,bees - Larrea flowers with annuals,other
## Larrea flowers with annuals,bees - Larrea flowers without annuals,other
## Larrea flowers without annuals,bees - Annual flowers in open,flies
## Larrea flowers without annuals,bees - Annual flowers under Ambrosia,flies
## Larrea flowers without annuals,bees - Annual flowers under Larrea,flies
## Larrea flowers without annuals,bees - Larrea flowers with annuals,flies
## Larrea flowers without annuals,bees - Larrea flowers without annuals,flies
## Larrea flowers without annuals,bees - Annual flowers in open,other
## Larrea flowers without annuals,bees - Annual flowers under Ambrosia,other
## Larrea flowers without annuals,bees - Annual flowers under Larrea,other
## Larrea flowers without annuals,bees - Larrea flowers with annuals,other
## Larrea flowers without annuals,bees - Larrea flowers without annuals,other
## Annual flowers in open,flies - Annual flowers under Ambrosia,flies
## Annual flowers in open,flies - Annual flowers under Larrea,flies
## Annual flowers in open,flies - Larrea flowers with annuals,flies
## Annual flowers in open,flies - Larrea flowers without annuals,flies
## Annual flowers in open,flies - Annual flowers in open,other
## Annual flowers in open,flies - Annual flowers under Ambrosia,other
## Annual flowers in open,flies - Annual flowers under Larrea,other
## Annual flowers in open,flies - Larrea flowers with annuals,other
## Annual flowers in open,flies - Larrea flowers without annuals,other
## Annual flowers under Ambrosia,flies - Annual flowers under Larrea,flies
## Annual flowers under Ambrosia,flies - Larrea flowers with annuals,flies
## Annual flowers under Ambrosia,flies - Larrea flowers without annuals,flies
## Annual flowers under Ambrosia,flies - Annual flowers in open,other
## Annual flowers under Ambrosia,flies - Annual flowers under Ambrosia,other
## Annual flowers under Ambrosia,flies - Annual flowers under Larrea,other
## Annual flowers under Ambrosia,flies - Larrea flowers with annuals,other
## Annual flowers under Ambrosia,flies - Larrea flowers without annuals,other
## Annual flowers under Larrea,flies - Larrea flowers with annuals,flies
## Annual flowers under Larrea,flies - Larrea flowers without annuals,flies
## Annual flowers under Larrea,flies - Annual flowers in open,other
## Annual flowers under Larrea,flies - Annual flowers under Ambrosia,other
## Annual flowers under Larrea,flies - Annual flowers under Larrea,other
## Annual flowers under Larrea,flies - Larrea flowers with annuals,other
## Annual flowers under Larrea,flies - Larrea flowers without annuals,other
## Larrea flowers with annuals,flies - Larrea flowers without annuals,flies
## Larrea flowers with annuals,flies - Annual flowers in open,other
## Larrea flowers with annuals,flies - Annual flowers under Ambrosia,other
## Larrea flowers with annuals,flies - Annual flowers under Larrea,other
## Larrea flowers with annuals,flies - Larrea flowers with annuals,other
## Larrea flowers with annuals,flies - Larrea flowers without annuals,other
## Larrea flowers without annuals,flies - Annual flowers in open,other
## Larrea flowers without annuals,flies - Annual flowers under Ambrosia,other
## Larrea flowers without annuals,flies - Annual flowers under Larrea,other
## Larrea flowers without annuals,flies - Larrea flowers with annuals,other
## Larrea flowers without annuals,flies - Larrea flowers without annuals,other
## Annual flowers in open,other - Annual flowers under Ambrosia,other
## Annual flowers in open,other - Annual flowers under Larrea,other
## Annual flowers in open,other - Larrea flowers with annuals,other
## Annual flowers in open,other - Larrea flowers without annuals,other
## Annual flowers under Ambrosia,other - Annual flowers under Larrea,other
## Annual flowers under Ambrosia,other - Larrea flowers with annuals,other
## Annual flowers under Ambrosia,other - Larrea flowers without annuals,other
## Annual flowers under Larrea,other - Larrea flowers with annuals,other
## Annual flowers under Larrea,other - Larrea flowers without annuals,other
## Larrea flowers with annuals,other - Larrea flowers without annuals,other
## estimate SE df z.ratio p.value
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
##
## Results are averaged over the levels of: rep
## P value adjustment: tukey method for comparing a family of 15 estimatesModel: all with additive terms
#Additive-term models for all insect taxa####
#visitations
m <- glm(rate.per.flower~net.treatment + insect.RTU %in% rep + mean.temp, family = "Gamma", data = freq.2015)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: Gamma, link: inverse
##
## Response: rate.per.flower
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 260 585.41
## net.treatment 3 246.249 257 339.16 < 2.2e-16 ***
## mean.temp 1 20.467 256 318.70 6.385e-05 ***
## insect.RTU:rep 11 21.037 245 297.66 0.1259
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1b1 <- AIC(m)
require(lsmeans)
lsmeans(m, pairwise~net.treatment:insect.RTU, adjust="tukey")## $lsmeans
## net.treatment insect.RTU lsmean SE df
## Annual flowers in open bees 5.193851 1.0253223 NA
## Annual flowers under Larrea bees 2.051491 0.4814461 NA
## Larrea flowers with annuals bees 35.017207 5.4782225 NA
## Larrea flowers without annuals bees 21.940192 3.5381215 NA
## Annual flowers in open flies 7.156606 1.1501339 NA
## Annual flowers under Larrea flies 4.014245 0.8558823 NA
## Larrea flowers with annuals flies 36.979962 5.5062802 NA
## Larrea flowers without annuals flies 23.902946 3.5733777 NA
## Annual flowers in open other 7.881104 1.3057629 NA
## Annual flowers under Larrea other 4.738744 1.0524992 NA
## Larrea flowers with annuals other 37.704460 5.5443877 NA
## Larrea flowers without annuals other 24.627445 3.6601950 NA
## asymp.LCL asymp.UCL
## 3.184257 7.203446
## 1.107874 2.995108
## 24.280089 45.754326
## 15.005602 28.874783
## 4.902385 9.410826
## 2.336747 5.691744
## 26.187851 47.772072
## 16.899255 30.906638
## 5.321856 10.440352
## 2.675883 6.801604
## 26.837660 48.571260
## 17.453594 31.801295
##
## Results are averaged over the levels of: rep
## Results are given on the inverse (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast
## Annual flowers in open,bees - Annual flowers under Larrea,bees
## Annual flowers in open,bees - Larrea flowers with annuals,bees
## Annual flowers in open,bees - Larrea flowers without annuals,bees
## Annual flowers in open,bees - Annual flowers in open,flies
## Annual flowers in open,bees - Annual flowers under Larrea,flies
## Annual flowers in open,bees - Larrea flowers with annuals,flies
## Annual flowers in open,bees - Larrea flowers without annuals,flies
## Annual flowers in open,bees - Annual flowers in open,other
## Annual flowers in open,bees - Annual flowers under Larrea,other
## Annual flowers in open,bees - Larrea flowers with annuals,other
## Annual flowers in open,bees - Larrea flowers without annuals,other
## Annual flowers under Larrea,bees - Larrea flowers with annuals,bees
## Annual flowers under Larrea,bees - Larrea flowers without annuals,bees
## Annual flowers under Larrea,bees - Annual flowers in open,flies
## Annual flowers under Larrea,bees - Annual flowers under Larrea,flies
## Annual flowers under Larrea,bees - Larrea flowers with annuals,flies
## Annual flowers under Larrea,bees - Larrea flowers without annuals,flies
## Annual flowers under Larrea,bees - Annual flowers in open,other
## Annual flowers under Larrea,bees - Annual flowers under Larrea,other
## Annual flowers under Larrea,bees - Larrea flowers with annuals,other
## Annual flowers under Larrea,bees - Larrea flowers without annuals,other
## Larrea flowers with annuals,bees - Larrea flowers without annuals,bees
## Larrea flowers with annuals,bees - Annual flowers in open,flies
## Larrea flowers with annuals,bees - Annual flowers under Larrea,flies
## Larrea flowers with annuals,bees - Larrea flowers with annuals,flies
## Larrea flowers with annuals,bees - Larrea flowers without annuals,flies
## Larrea flowers with annuals,bees - Annual flowers in open,other
## Larrea flowers with annuals,bees - Annual flowers under Larrea,other
## Larrea flowers with annuals,bees - Larrea flowers with annuals,other
## Larrea flowers with annuals,bees - Larrea flowers without annuals,other
## Larrea flowers without annuals,bees - Annual flowers in open,flies
## Larrea flowers without annuals,bees - Annual flowers under Larrea,flies
## Larrea flowers without annuals,bees - Larrea flowers with annuals,flies
## Larrea flowers without annuals,bees - Larrea flowers without annuals,flies
## Larrea flowers without annuals,bees - Annual flowers in open,other
## Larrea flowers without annuals,bees - Annual flowers under Larrea,other
## Larrea flowers without annuals,bees - Larrea flowers with annuals,other
## Larrea flowers without annuals,bees - Larrea flowers without annuals,other
## Annual flowers in open,flies - Annual flowers under Larrea,flies
## Annual flowers in open,flies - Larrea flowers with annuals,flies
## Annual flowers in open,flies - Larrea flowers without annuals,flies
## Annual flowers in open,flies - Annual flowers in open,other
## Annual flowers in open,flies - Annual flowers under Larrea,other
## Annual flowers in open,flies - Larrea flowers with annuals,other
## Annual flowers in open,flies - Larrea flowers without annuals,other
## Annual flowers under Larrea,flies - Larrea flowers with annuals,flies
## Annual flowers under Larrea,flies - Larrea flowers without annuals,flies
## Annual flowers under Larrea,flies - Annual flowers in open,other
## Annual flowers under Larrea,flies - Annual flowers under Larrea,other
## Annual flowers under Larrea,flies - Larrea flowers with annuals,other
## Annual flowers under Larrea,flies - Larrea flowers without annuals,other
## Larrea flowers with annuals,flies - Larrea flowers without annuals,flies
## Larrea flowers with annuals,flies - Annual flowers in open,other
## Larrea flowers with annuals,flies - Annual flowers under Larrea,other
## Larrea flowers with annuals,flies - Larrea flowers with annuals,other
## Larrea flowers with annuals,flies - Larrea flowers without annuals,other
## Larrea flowers without annuals,flies - Annual flowers in open,other
## Larrea flowers without annuals,flies - Annual flowers under Larrea,other
## Larrea flowers without annuals,flies - Larrea flowers with annuals,other
## Larrea flowers without annuals,flies - Larrea flowers without annuals,other
## Annual flowers in open,other - Annual flowers under Larrea,other
## Annual flowers in open,other - Larrea flowers with annuals,other
## Annual flowers in open,other - Larrea flowers without annuals,other
## Annual flowers under Larrea,other - Larrea flowers with annuals,other
## Annual flowers under Larrea,other - Larrea flowers without annuals,other
## Larrea flowers with annuals,other - Larrea flowers without annuals,other
## estimate SE df z.ratio p.value
## 3.1423602 1.172804 NA 2.679 0.2364
## -29.8233561 5.605698 NA -5.320 <.0001
## -16.7463409 3.704233 NA -4.521 0.0004
## -1.9627541 0.840959 NA -2.334 0.4521
## 1.1796061 1.520494 NA 0.776 0.9998
## -31.7861102 5.671661 NA -5.604 <.0001
## -18.7090950 3.795755 NA -4.929 0.0001
## -2.6872524 1.039857 NA -2.584 0.2885
## 0.4551078 1.636767 NA 0.278 1.0000
## -32.5106085 5.707954 NA -5.696 <.0001
## -19.4335934 3.876550 NA -5.013 <.0001
## -32.9657163 5.485023 NA -6.010 <.0001
## -19.8887011 3.552806 NA -5.598 <.0001
## -5.1051143 1.361418 NA -3.750 0.0097
## -1.9627541 0.840959 NA -2.334 0.4521
## -34.9284704 5.531740 NA -6.314 <.0001
## -21.8514553 3.616576 NA -6.042 <.0001
## -5.8296126 1.494837 NA -3.900 0.0055
## -2.6872524 1.039857 NA -2.584 0.2885
## -35.6529687 5.569572 NA -6.401 <.0001
## -22.5759536 3.702228 NA -6.098 <.0001
## 13.0770151 6.501748 NA 2.011 0.6858
## 27.8606020 5.665191 NA 4.918 0.0001
## 31.0029622 5.566438 NA 5.570 <.0001
## -1.9627541 0.840959 NA -2.334 0.4521
## 11.1142610 6.551524 NA 1.696 0.8703
## 27.1361037 5.694697 NA 4.765 0.0001
## 30.2784639 5.595841 NA 5.411 <.0001
## -2.6872524 1.039857 NA -2.584 0.2885
## 10.3897627 6.595714 NA 1.575 0.9182
## 14.7835868 3.801230 NA 3.889 0.0057
## 17.9259470 3.685060 NA 4.864 0.0001
## -15.0397693 6.560291 NA -2.293 0.4819
## -1.9627541 0.840959 NA -2.334 0.4521
## 14.0590885 3.818069 NA 3.682 0.0124
## 17.2014487 3.701483 NA 4.647 0.0002
## -15.7642676 6.573022 NA -2.398 0.4070
## -2.6872524 1.039857 NA -2.584 0.2885
## 3.1423602 1.172804 NA 2.679 0.2364
## -29.8233561 5.605698 NA -5.320 <.0001
## -16.7463409 3.704233 NA -4.521 0.0004
## -0.7244983 1.237830 NA -0.585 1.0000
## 2.4178619 1.703145 NA 1.420 0.9600
## -30.5478544 5.744126 NA -5.318 <.0001
## -17.4708392 3.936922 NA -4.438 0.0006
## -32.9657163 5.485023 NA -6.010 <.0001
## -19.8887011 3.552806 NA -5.598 <.0001
## -3.8668585 1.707244 NA -2.265 0.5019
## -0.7244983 1.237830 NA -0.585 1.0000
## -33.6902146 5.627041 NA -5.987 <.0001
## -20.6131995 3.795713 NA -5.431 <.0001
## 13.0770151 6.501748 NA 2.011 0.6858
## 29.0988578 5.737349 NA 5.072 <.0001
## 32.2412180 5.618880 NA 5.738 <.0001
## -0.7244983 1.237830 NA -0.585 1.0000
## 12.3525168 6.634142 NA 1.862 0.7829
## 16.0218426 3.873987 NA 4.136 0.0021
## 19.1642028 3.728522 NA 5.140 <.0001
## -13.8015135 6.602883 NA -2.090 0.6299
## -0.7244983 1.237830 NA -0.585 1.0000
## 3.1423602 1.172804 NA 2.679 0.2364
## -29.8233561 5.605698 NA -5.320 <.0001
## -16.7463409 3.704233 NA -4.521 0.0004
## -32.9657163 5.485023 NA -6.010 <.0001
## -19.8887011 3.552806 NA -5.598 <.0001
## 13.0770151 6.501748 NA 2.011 0.6858
##
## Results are averaged over the levels of: rep
## P value adjustment: tukey method for comparing a family of 12 estimatesm <- glm(rate.per.flower~net.treatment + insect.RTU %in% rep + mean.temp, family = "Gamma", data = freq.2016)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: Gamma, link: inverse
##
## Response: rate.per.flower
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 229 795.36
## net.treatment 4 559.99 225 235.36 <2e-16 ***
## mean.temp 1 0.07 224 235.29 0.7035
## insect.RTU:rep 12 138.72 212 96.58 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1b2 <- AIC(m)
lsmeans(m, pairwise~net.treatment:insect.RTU, adjust="tukey")## $lsmeans
## net.treatment insect.RTU lsmean SE df
## Annual flowers in open bees 1.917555 0.7069774 NA
## Annual flowers under Ambrosia bees 1.735953 0.7039591 NA
## Annual flowers under Larrea bees 1.501888 0.6971146 NA
## Larrea flowers with annuals bees 126.991036 14.3627730 NA
## Larrea flowers without annuals bees 118.744435 12.0869516 NA
## Annual flowers in open flies NA NA NA
## Annual flowers under Ambrosia flies NA NA NA
## Annual flowers under Larrea flies NA NA NA
## Larrea flowers with annuals flies NA NA NA
## Larrea flowers without annuals flies NA NA NA
## Annual flowers in open other NA NA NA
## Annual flowers under Ambrosia other NA NA NA
## Annual flowers under Larrea other NA NA NA
## Larrea flowers with annuals other NA NA NA
## Larrea flowers without annuals other NA NA NA
## asymp.LCL asymp.UCL
## 0.5319052 3.303206
## 0.3562187 3.115688
## 0.1355683 2.868207
## 98.8405184 155.141554
## 95.0544448 142.434424
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
##
## Results are averaged over the levels of: rep
## Results are given on the inverse (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast
## Annual flowers in open,bees - Annual flowers under Ambrosia,bees
## Annual flowers in open,bees - Annual flowers under Larrea,bees
## Annual flowers in open,bees - Larrea flowers with annuals,bees
## Annual flowers in open,bees - Larrea flowers without annuals,bees
## Annual flowers in open,bees - Annual flowers in open,flies
## Annual flowers in open,bees - Annual flowers under Ambrosia,flies
## Annual flowers in open,bees - Annual flowers under Larrea,flies
## Annual flowers in open,bees - Larrea flowers with annuals,flies
## Annual flowers in open,bees - Larrea flowers without annuals,flies
## Annual flowers in open,bees - Annual flowers in open,other
## Annual flowers in open,bees - Annual flowers under Ambrosia,other
## Annual flowers in open,bees - Annual flowers under Larrea,other
## Annual flowers in open,bees - Larrea flowers with annuals,other
## Annual flowers in open,bees - Larrea flowers without annuals,other
## Annual flowers under Ambrosia,bees - Annual flowers under Larrea,bees
## Annual flowers under Ambrosia,bees - Larrea flowers with annuals,bees
## Annual flowers under Ambrosia,bees - Larrea flowers without annuals,bees
## Annual flowers under Ambrosia,bees - Annual flowers in open,flies
## Annual flowers under Ambrosia,bees - Annual flowers under Ambrosia,flies
## Annual flowers under Ambrosia,bees - Annual flowers under Larrea,flies
## Annual flowers under Ambrosia,bees - Larrea flowers with annuals,flies
## Annual flowers under Ambrosia,bees - Larrea flowers without annuals,flies
## Annual flowers under Ambrosia,bees - Annual flowers in open,other
## Annual flowers under Ambrosia,bees - Annual flowers under Ambrosia,other
## Annual flowers under Ambrosia,bees - Annual flowers under Larrea,other
## Annual flowers under Ambrosia,bees - Larrea flowers with annuals,other
## Annual flowers under Ambrosia,bees - Larrea flowers without annuals,other
## Annual flowers under Larrea,bees - Larrea flowers with annuals,bees
## Annual flowers under Larrea,bees - Larrea flowers without annuals,bees
## Annual flowers under Larrea,bees - Annual flowers in open,flies
## Annual flowers under Larrea,bees - Annual flowers under Ambrosia,flies
## Annual flowers under Larrea,bees - Annual flowers under Larrea,flies
## Annual flowers under Larrea,bees - Larrea flowers with annuals,flies
## Annual flowers under Larrea,bees - Larrea flowers without annuals,flies
## Annual flowers under Larrea,bees - Annual flowers in open,other
## Annual flowers under Larrea,bees - Annual flowers under Ambrosia,other
## Annual flowers under Larrea,bees - Annual flowers under Larrea,other
## Annual flowers under Larrea,bees - Larrea flowers with annuals,other
## Annual flowers under Larrea,bees - Larrea flowers without annuals,other
## Larrea flowers with annuals,bees - Larrea flowers without annuals,bees
## Larrea flowers with annuals,bees - Annual flowers in open,flies
## Larrea flowers with annuals,bees - Annual flowers under Ambrosia,flies
## Larrea flowers with annuals,bees - Annual flowers under Larrea,flies
## Larrea flowers with annuals,bees - Larrea flowers with annuals,flies
## Larrea flowers with annuals,bees - Larrea flowers without annuals,flies
## Larrea flowers with annuals,bees - Annual flowers in open,other
## Larrea flowers with annuals,bees - Annual flowers under Ambrosia,other
## Larrea flowers with annuals,bees - Annual flowers under Larrea,other
## Larrea flowers with annuals,bees - Larrea flowers with annuals,other
## Larrea flowers with annuals,bees - Larrea flowers without annuals,other
## Larrea flowers without annuals,bees - Annual flowers in open,flies
## Larrea flowers without annuals,bees - Annual flowers under Ambrosia,flies
## Larrea flowers without annuals,bees - Annual flowers under Larrea,flies
## Larrea flowers without annuals,bees - Larrea flowers with annuals,flies
## Larrea flowers without annuals,bees - Larrea flowers without annuals,flies
## Larrea flowers without annuals,bees - Annual flowers in open,other
## Larrea flowers without annuals,bees - Annual flowers under Ambrosia,other
## Larrea flowers without annuals,bees - Annual flowers under Larrea,other
## Larrea flowers without annuals,bees - Larrea flowers with annuals,other
## Larrea flowers without annuals,bees - Larrea flowers without annuals,other
## Annual flowers in open,flies - Annual flowers under Ambrosia,flies
## Annual flowers in open,flies - Annual flowers under Larrea,flies
## Annual flowers in open,flies - Larrea flowers with annuals,flies
## Annual flowers in open,flies - Larrea flowers without annuals,flies
## Annual flowers in open,flies - Annual flowers in open,other
## Annual flowers in open,flies - Annual flowers under Ambrosia,other
## Annual flowers in open,flies - Annual flowers under Larrea,other
## Annual flowers in open,flies - Larrea flowers with annuals,other
## Annual flowers in open,flies - Larrea flowers without annuals,other
## Annual flowers under Ambrosia,flies - Annual flowers under Larrea,flies
## Annual flowers under Ambrosia,flies - Larrea flowers with annuals,flies
## Annual flowers under Ambrosia,flies - Larrea flowers without annuals,flies
## Annual flowers under Ambrosia,flies - Annual flowers in open,other
## Annual flowers under Ambrosia,flies - Annual flowers under Ambrosia,other
## Annual flowers under Ambrosia,flies - Annual flowers under Larrea,other
## Annual flowers under Ambrosia,flies - Larrea flowers with annuals,other
## Annual flowers under Ambrosia,flies - Larrea flowers without annuals,other
## Annual flowers under Larrea,flies - Larrea flowers with annuals,flies
## Annual flowers under Larrea,flies - Larrea flowers without annuals,flies
## Annual flowers under Larrea,flies - Annual flowers in open,other
## Annual flowers under Larrea,flies - Annual flowers under Ambrosia,other
## Annual flowers under Larrea,flies - Annual flowers under Larrea,other
## Annual flowers under Larrea,flies - Larrea flowers with annuals,other
## Annual flowers under Larrea,flies - Larrea flowers without annuals,other
## Larrea flowers with annuals,flies - Larrea flowers without annuals,flies
## Larrea flowers with annuals,flies - Annual flowers in open,other
## Larrea flowers with annuals,flies - Annual flowers under Ambrosia,other
## Larrea flowers with annuals,flies - Annual flowers under Larrea,other
## Larrea flowers with annuals,flies - Larrea flowers with annuals,other
## Larrea flowers with annuals,flies - Larrea flowers without annuals,other
## Larrea flowers without annuals,flies - Annual flowers in open,other
## Larrea flowers without annuals,flies - Annual flowers under Ambrosia,other
## Larrea flowers without annuals,flies - Annual flowers under Larrea,other
## Larrea flowers without annuals,flies - Larrea flowers with annuals,other
## Larrea flowers without annuals,flies - Larrea flowers without annuals,other
## Annual flowers in open,other - Annual flowers under Ambrosia,other
## Annual flowers in open,other - Annual flowers under Larrea,other
## Annual flowers in open,other - Larrea flowers with annuals,other
## Annual flowers in open,other - Larrea flowers without annuals,other
## Annual flowers under Ambrosia,other - Annual flowers under Larrea,other
## Annual flowers under Ambrosia,other - Larrea flowers with annuals,other
## Annual flowers under Ambrosia,other - Larrea flowers without annuals,other
## Annual flowers under Larrea,other - Larrea flowers with annuals,other
## Annual flowers under Larrea,other - Larrea flowers without annuals,other
## Larrea flowers with annuals,other - Larrea flowers without annuals,other
## estimate SE df z.ratio p.value
## 0.1816023 0.2121870 NA 0.856 0.9999
## 0.4156677 0.1876153 NA 2.216 0.6536
## -125.0734807 14.3469797 NA -8.718 <.0001
## -116.8268790 12.0693792 NA -9.680 <.0001
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## 0.2340654 0.1687083 NA 1.387 0.9885
## -125.2550830 14.3466982 NA -8.731 <.0001
## -117.0084813 12.0681419 NA -9.696 <.0001
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## -125.4891484 14.3464421 NA -8.747 <.0001
## -117.2425467 12.0678470 NA -9.715 <.0001
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## 8.2466017 18.7376661 NA 0.440 1.0000
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## 0.1816023 0.2121870 NA 0.856 0.9999
## 0.4156677 0.1876153 NA 2.216 0.6536
## -125.0734807 14.3469797 NA -8.718 <.0001
## -116.8268790 12.0693792 NA -9.680 <.0001
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## 0.2340654 0.1687083 NA 1.387 0.9885
## -125.2550830 14.3466982 NA -8.731 <.0001
## -117.0084813 12.0681419 NA -9.696 <.0001
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## -125.4891484 14.3464421 NA -8.747 <.0001
## -117.2425467 12.0678470 NA -9.715 <.0001
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## 8.2466017 18.7376661 NA 0.440 1.0000
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## 0.1816023 0.2121870 NA 0.856 0.9999
## 0.4156677 0.1876153 NA 2.216 0.6536
## -125.0734807 14.3469797 NA -8.718 <.0001
## -116.8268790 12.0693792 NA -9.680 <.0001
## 0.2340654 0.1687083 NA 1.387 0.9885
## -125.2550830 14.3466982 NA -8.731 <.0001
## -117.0084813 12.0681419 NA -9.696 <.0001
## -125.4891484 14.3464421 NA -8.747 <.0001
## -117.2425467 12.0678470 NA -9.715 <.0001
## 8.2466017 18.7376661 NA 0.440 1.0000
##
## Results are averaged over the levels of: rep
## P value adjustment: tukey method for comparing a family of 15 estimatesm <- glm(rate.per.flower.mean.time~net.treatment + insect.RTU %in% rep + mean.temp, family = "Gamma", data = freq.2015)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: Gamma, link: inverse
##
## Response: rate.per.flower.mean.time
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 260 317.65
## net.treatment 3 123.387 257 194.26 < 2.2e-16 ***
## mean.temp 1 19.375 256 174.88 8.369e-08 ***
## insect.RTU:rep 11 26.429 245 148.46 4.945e-05 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1b3 <- AIC(m)
lsmeans(m, pairwise~net.treatment:insect.RTU, adjust="tukey")## $lsmeans
## net.treatment insect.RTU lsmean SE df
## Annual flowers in open bees 6.659569 0.9681502 NA
## Annual flowers under Larrea bees 2.724917 0.4678877 NA
## Larrea flowers with annuals bees 16.361146 2.0659595 NA
## Larrea flowers without annuals bees 18.566590 2.2576712 NA
## Annual flowers in open flies 9.540596 1.0998780 NA
## Annual flowers under Larrea flies 5.605945 0.8353173 NA
## Larrea flowers with annuals flies 19.242173 2.1414385 NA
## Larrea flowers without annuals flies 21.447617 2.3115787 NA
## Annual flowers in open other 11.213263 1.3367868 NA
## Annual flowers under Larrea other 7.278612 1.1301453 NA
## Larrea flowers with annuals other 20.914841 2.2808068 NA
## Larrea flowers without annuals other 23.120285 2.4789352 NA
## asymp.LCL asymp.UCL
## 4.762029 8.557108
## 1.807874 3.641960
## 12.311940 20.410352
## 14.141636 22.991544
## 7.384874 11.696317
## 3.968753 7.243136
## 15.045031 23.439316
## 16.917006 25.978228
## 8.593209 13.833317
## 5.063568 9.493656
## 16.444542 25.385140
## 18.261661 27.978908
##
## Results are averaged over the levels of: rep
## Results are given on the inverse (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast
## Annual flowers in open,bees - Annual flowers under Larrea,bees
## Annual flowers in open,bees - Larrea flowers with annuals,bees
## Annual flowers in open,bees - Larrea flowers without annuals,bees
## Annual flowers in open,bees - Annual flowers in open,flies
## Annual flowers in open,bees - Annual flowers under Larrea,flies
## Annual flowers in open,bees - Larrea flowers with annuals,flies
## Annual flowers in open,bees - Larrea flowers without annuals,flies
## Annual flowers in open,bees - Annual flowers in open,other
## Annual flowers in open,bees - Annual flowers under Larrea,other
## Annual flowers in open,bees - Larrea flowers with annuals,other
## Annual flowers in open,bees - Larrea flowers without annuals,other
## Annual flowers under Larrea,bees - Larrea flowers with annuals,bees
## Annual flowers under Larrea,bees - Larrea flowers without annuals,bees
## Annual flowers under Larrea,bees - Annual flowers in open,flies
## Annual flowers under Larrea,bees - Annual flowers under Larrea,flies
## Annual flowers under Larrea,bees - Larrea flowers with annuals,flies
## Annual flowers under Larrea,bees - Larrea flowers without annuals,flies
## Annual flowers under Larrea,bees - Annual flowers in open,other
## Annual flowers under Larrea,bees - Annual flowers under Larrea,other
## Annual flowers under Larrea,bees - Larrea flowers with annuals,other
## Annual flowers under Larrea,bees - Larrea flowers without annuals,other
## Larrea flowers with annuals,bees - Larrea flowers without annuals,bees
## Larrea flowers with annuals,bees - Annual flowers in open,flies
## Larrea flowers with annuals,bees - Annual flowers under Larrea,flies
## Larrea flowers with annuals,bees - Larrea flowers with annuals,flies
## Larrea flowers with annuals,bees - Larrea flowers without annuals,flies
## Larrea flowers with annuals,bees - Annual flowers in open,other
## Larrea flowers with annuals,bees - Annual flowers under Larrea,other
## Larrea flowers with annuals,bees - Larrea flowers with annuals,other
## Larrea flowers with annuals,bees - Larrea flowers without annuals,other
## Larrea flowers without annuals,bees - Annual flowers in open,flies
## Larrea flowers without annuals,bees - Annual flowers under Larrea,flies
## Larrea flowers without annuals,bees - Larrea flowers with annuals,flies
## Larrea flowers without annuals,bees - Larrea flowers without annuals,flies
## Larrea flowers without annuals,bees - Annual flowers in open,other
## Larrea flowers without annuals,bees - Annual flowers under Larrea,other
## Larrea flowers without annuals,bees - Larrea flowers with annuals,other
## Larrea flowers without annuals,bees - Larrea flowers without annuals,other
## Annual flowers in open,flies - Annual flowers under Larrea,flies
## Annual flowers in open,flies - Larrea flowers with annuals,flies
## Annual flowers in open,flies - Larrea flowers without annuals,flies
## Annual flowers in open,flies - Annual flowers in open,other
## Annual flowers in open,flies - Annual flowers under Larrea,other
## Annual flowers in open,flies - Larrea flowers with annuals,other
## Annual flowers in open,flies - Larrea flowers without annuals,other
## Annual flowers under Larrea,flies - Larrea flowers with annuals,flies
## Annual flowers under Larrea,flies - Larrea flowers without annuals,flies
## Annual flowers under Larrea,flies - Annual flowers in open,other
## Annual flowers under Larrea,flies - Annual flowers under Larrea,other
## Annual flowers under Larrea,flies - Larrea flowers with annuals,other
## Annual flowers under Larrea,flies - Larrea flowers without annuals,other
## Larrea flowers with annuals,flies - Larrea flowers without annuals,flies
## Larrea flowers with annuals,flies - Annual flowers in open,other
## Larrea flowers with annuals,flies - Annual flowers under Larrea,other
## Larrea flowers with annuals,flies - Larrea flowers with annuals,other
## Larrea flowers with annuals,flies - Larrea flowers without annuals,other
## Larrea flowers without annuals,flies - Annual flowers in open,other
## Larrea flowers without annuals,flies - Annual flowers under Larrea,other
## Larrea flowers without annuals,flies - Larrea flowers with annuals,other
## Larrea flowers without annuals,flies - Larrea flowers without annuals,other
## Annual flowers in open,other - Annual flowers under Larrea,other
## Annual flowers in open,other - Larrea flowers with annuals,other
## Annual flowers in open,other - Larrea flowers without annuals,other
## Annual flowers under Larrea,other - Larrea flowers with annuals,other
## Annual flowers under Larrea,other - Larrea flowers without annuals,other
## Larrea flowers with annuals,other - Larrea flowers without annuals,other
## estimate SE df z.ratio p.value
## 3.9346511 1.1204197 NA 3.512 0.0226
## -9.7015776 2.3473615 NA -4.133 0.0021
## -11.9070213 2.4729754 NA -4.815 0.0001
## -2.8810272 0.8123538 NA -3.547 0.0201
## 1.0536240 1.4565982 NA 0.723 0.9999
## -12.5826048 2.4930259 NA -5.047 <.0001
## -14.7880485 2.5979657 NA -5.692 <.0001
## -4.5536947 1.1138844 NA -4.088 0.0026
## -0.6190436 1.6445985 NA -0.376 1.0000
## -14.2552723 2.6143931 NA -5.453 <.0001
## -16.4607161 2.7485818 NA -5.989 <.0001
## -13.6362287 2.0872485 NA -6.533 <.0001
## -15.8416725 2.2831299 NA -6.939 <.0001
## -6.8156783 1.3072260 NA -5.214 <.0001
## -2.8810272 0.8123538 NA -3.547 0.0201
## -16.5172559 2.2034653 NA -7.496 <.0001
## -18.7226997 2.3748856 NA -7.884 <.0001
## -8.4883459 1.5124330 NA -5.612 <.0001
## -4.5536947 1.1138844 NA -4.088 0.0026
## -18.1899235 2.3394287 NA -7.775 <.0001
## -20.3953672 2.5383365 NA -8.035 <.0001
## -2.2054437 3.0280952 NA -0.728 0.9999
## 6.8205504 2.4748477 NA 2.756 0.1992
## 10.7552016 2.2754759 NA 4.727 0.0001
## -2.8810272 0.8123538 NA -3.547 0.0201
## -5.0864709 3.1237839 NA -1.628 0.8990
## 5.1478828 2.5819832 NA 1.994 0.6979
## 9.0825340 2.3920207 NA 3.797 0.0081
## -4.5536947 1.1138844 NA -4.088 0.0026
## -6.7591385 3.2441098 NA -2.084 0.6347
## 9.0259942 2.6079927 NA 3.461 0.0269
## 12.9606453 2.4708541 NA 5.245 <.0001
## -0.6755834 3.1465112 NA -0.215 1.0000
## -2.8810272 0.8123538 NA -3.547 0.0201
## 7.3533266 2.6754418 NA 2.748 0.2027
## 11.2879777 2.5423787 NA 4.440 0.0006
## -2.3482510 3.2087302 NA -0.732 0.9999
## -4.5536947 1.1138844 NA -4.088 0.0026
## 3.9346511 1.1204197 NA 3.512 0.0226
## -9.7015776 2.3473615 NA -4.133 0.0021
## -11.9070213 2.4729754 NA -4.815 0.0001
## -1.6726676 1.2911285 NA -1.296 0.9799
## 2.2619836 1.7101343 NA 1.323 0.9764
## -11.3742452 2.6862934 NA -4.234 0.0014
## -13.5796889 2.8296778 NA -4.799 0.0001
## -13.6362287 2.0872485 NA -6.533 <.0001
## -15.8416725 2.2831299 NA -6.939 <.0001
## -5.6073187 1.7088438 NA -3.281 0.0480
## -1.6726676 1.2911285 NA -1.296 0.9799
## -15.3088963 2.4618015 NA -6.219 <.0001
## -17.5143401 2.6649476 NA -6.572 <.0001
## -2.2054437 3.0280952 NA -0.728 0.9999
## 8.0289100 2.6717158 NA 3.005 0.1069
## 11.9635612 2.4467881 NA 4.889 0.0001
## -1.6726676 1.2911285 NA -1.296 0.9799
## -3.8781113 3.3199061 NA -1.168 0.9913
## 10.2343538 2.7492114 NA 3.723 0.0107
## 14.1690049 2.5802024 NA 5.491 <.0001
## 0.5327762 3.2635824 NA 0.163 1.0000
## -1.6726676 1.2911285 NA -1.296 0.9799
## 3.9346511 1.1204197 NA 3.512 0.0226
## -9.7015776 2.3473615 NA -4.133 0.0021
## -11.9070213 2.4729754 NA -4.815 0.0001
## -13.6362287 2.0872485 NA -6.533 <.0001
## -15.8416725 2.2831299 NA -6.939 <.0001
## -2.2054437 3.0280952 NA -0.728 0.9999
##
## Results are averaged over the levels of: rep
## P value adjustment: tukey method for comparing a family of 12 estimatesm <- glm(rate.per.flower.mean.time~net.treatment + insect.RTU %in% rep + mean.temp, family = "Gamma", data = freq.2016)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: Gamma, link: inverse
##
## Response: rate.per.flower.mean.time
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 229 522.69
## net.treatment 4 285.306 225 237.39 <2e-16 ***
## mean.temp 1 1.162 224 236.22 0.1108
## insect.RTU:rep 12 141.614 212 94.61 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1b4 <- AIC(m)
lsmeans(m, pairwise~net.treatment:insect.RTU, adjust="tukey")## $lsmeans
## net.treatment insect.RTU lsmean SE df
## Annual flowers in open bees 2.768635 0.9862383 NA
## Annual flowers under Ambrosia bees 2.367412 0.9789266 NA
## Annual flowers under Larrea bees 2.134728 0.9727264 NA
## Larrea flowers with annuals bees 29.459929 3.6273995 NA
## Larrea flowers without annuals bees 26.774770 3.0945544 NA
## Annual flowers in open flies NA NA NA
## Annual flowers under Ambrosia flies NA NA NA
## Annual flowers under Larrea flies NA NA NA
## Larrea flowers with annuals flies NA NA NA
## Larrea flowers without annuals flies NA NA NA
## Annual flowers in open other NA NA NA
## Annual flowers under Ambrosia other NA NA NA
## Annual flowers under Larrea other NA NA NA
## Larrea flowers with annuals other NA NA NA
## Larrea flowers without annuals other NA NA NA
## asymp.LCL asymp.UCL
## 0.8356432 4.701626
## 0.4487515 4.286073
## 0.2282194 4.041237
## 22.3503563 36.569501
## 20.7095544 32.839985
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
##
## Results are averaged over the levels of: rep
## Results are given on the inverse (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast
## Annual flowers in open,bees - Annual flowers under Ambrosia,bees
## Annual flowers in open,bees - Annual flowers under Larrea,bees
## Annual flowers in open,bees - Larrea flowers with annuals,bees
## Annual flowers in open,bees - Larrea flowers without annuals,bees
## Annual flowers in open,bees - Annual flowers in open,flies
## Annual flowers in open,bees - Annual flowers under Ambrosia,flies
## Annual flowers in open,bees - Annual flowers under Larrea,flies
## Annual flowers in open,bees - Larrea flowers with annuals,flies
## Annual flowers in open,bees - Larrea flowers without annuals,flies
## Annual flowers in open,bees - Annual flowers in open,other
## Annual flowers in open,bees - Annual flowers under Ambrosia,other
## Annual flowers in open,bees - Annual flowers under Larrea,other
## Annual flowers in open,bees - Larrea flowers with annuals,other
## Annual flowers in open,bees - Larrea flowers without annuals,other
## Annual flowers under Ambrosia,bees - Annual flowers under Larrea,bees
## Annual flowers under Ambrosia,bees - Larrea flowers with annuals,bees
## Annual flowers under Ambrosia,bees - Larrea flowers without annuals,bees
## Annual flowers under Ambrosia,bees - Annual flowers in open,flies
## Annual flowers under Ambrosia,bees - Annual flowers under Ambrosia,flies
## Annual flowers under Ambrosia,bees - Annual flowers under Larrea,flies
## Annual flowers under Ambrosia,bees - Larrea flowers with annuals,flies
## Annual flowers under Ambrosia,bees - Larrea flowers without annuals,flies
## Annual flowers under Ambrosia,bees - Annual flowers in open,other
## Annual flowers under Ambrosia,bees - Annual flowers under Ambrosia,other
## Annual flowers under Ambrosia,bees - Annual flowers under Larrea,other
## Annual flowers under Ambrosia,bees - Larrea flowers with annuals,other
## Annual flowers under Ambrosia,bees - Larrea flowers without annuals,other
## Annual flowers under Larrea,bees - Larrea flowers with annuals,bees
## Annual flowers under Larrea,bees - Larrea flowers without annuals,bees
## Annual flowers under Larrea,bees - Annual flowers in open,flies
## Annual flowers under Larrea,bees - Annual flowers under Ambrosia,flies
## Annual flowers under Larrea,bees - Annual flowers under Larrea,flies
## Annual flowers under Larrea,bees - Larrea flowers with annuals,flies
## Annual flowers under Larrea,bees - Larrea flowers without annuals,flies
## Annual flowers under Larrea,bees - Annual flowers in open,other
## Annual flowers under Larrea,bees - Annual flowers under Ambrosia,other
## Annual flowers under Larrea,bees - Annual flowers under Larrea,other
## Annual flowers under Larrea,bees - Larrea flowers with annuals,other
## Annual flowers under Larrea,bees - Larrea flowers without annuals,other
## Larrea flowers with annuals,bees - Larrea flowers without annuals,bees
## Larrea flowers with annuals,bees - Annual flowers in open,flies
## Larrea flowers with annuals,bees - Annual flowers under Ambrosia,flies
## Larrea flowers with annuals,bees - Annual flowers under Larrea,flies
## Larrea flowers with annuals,bees - Larrea flowers with annuals,flies
## Larrea flowers with annuals,bees - Larrea flowers without annuals,flies
## Larrea flowers with annuals,bees - Annual flowers in open,other
## Larrea flowers with annuals,bees - Annual flowers under Ambrosia,other
## Larrea flowers with annuals,bees - Annual flowers under Larrea,other
## Larrea flowers with annuals,bees - Larrea flowers with annuals,other
## Larrea flowers with annuals,bees - Larrea flowers without annuals,other
## Larrea flowers without annuals,bees - Annual flowers in open,flies
## Larrea flowers without annuals,bees - Annual flowers under Ambrosia,flies
## Larrea flowers without annuals,bees - Annual flowers under Larrea,flies
## Larrea flowers without annuals,bees - Larrea flowers with annuals,flies
## Larrea flowers without annuals,bees - Larrea flowers without annuals,flies
## Larrea flowers without annuals,bees - Annual flowers in open,other
## Larrea flowers without annuals,bees - Annual flowers under Ambrosia,other
## Larrea flowers without annuals,bees - Annual flowers under Larrea,other
## Larrea flowers without annuals,bees - Larrea flowers with annuals,other
## Larrea flowers without annuals,bees - Larrea flowers without annuals,other
## Annual flowers in open,flies - Annual flowers under Ambrosia,flies
## Annual flowers in open,flies - Annual flowers under Larrea,flies
## Annual flowers in open,flies - Larrea flowers with annuals,flies
## Annual flowers in open,flies - Larrea flowers without annuals,flies
## Annual flowers in open,flies - Annual flowers in open,other
## Annual flowers in open,flies - Annual flowers under Ambrosia,other
## Annual flowers in open,flies - Annual flowers under Larrea,other
## Annual flowers in open,flies - Larrea flowers with annuals,other
## Annual flowers in open,flies - Larrea flowers without annuals,other
## Annual flowers under Ambrosia,flies - Annual flowers under Larrea,flies
## Annual flowers under Ambrosia,flies - Larrea flowers with annuals,flies
## Annual flowers under Ambrosia,flies - Larrea flowers without annuals,flies
## Annual flowers under Ambrosia,flies - Annual flowers in open,other
## Annual flowers under Ambrosia,flies - Annual flowers under Ambrosia,other
## Annual flowers under Ambrosia,flies - Annual flowers under Larrea,other
## Annual flowers under Ambrosia,flies - Larrea flowers with annuals,other
## Annual flowers under Ambrosia,flies - Larrea flowers without annuals,other
## Annual flowers under Larrea,flies - Larrea flowers with annuals,flies
## Annual flowers under Larrea,flies - Larrea flowers without annuals,flies
## Annual flowers under Larrea,flies - Annual flowers in open,other
## Annual flowers under Larrea,flies - Annual flowers under Ambrosia,other
## Annual flowers under Larrea,flies - Annual flowers under Larrea,other
## Annual flowers under Larrea,flies - Larrea flowers with annuals,other
## Annual flowers under Larrea,flies - Larrea flowers without annuals,other
## Larrea flowers with annuals,flies - Larrea flowers without annuals,flies
## Larrea flowers with annuals,flies - Annual flowers in open,other
## Larrea flowers with annuals,flies - Annual flowers under Ambrosia,other
## Larrea flowers with annuals,flies - Annual flowers under Larrea,other
## Larrea flowers with annuals,flies - Larrea flowers with annuals,other
## Larrea flowers with annuals,flies - Larrea flowers without annuals,other
## Larrea flowers without annuals,flies - Annual flowers in open,other
## Larrea flowers without annuals,flies - Annual flowers under Ambrosia,other
## Larrea flowers without annuals,flies - Annual flowers under Larrea,other
## Larrea flowers without annuals,flies - Larrea flowers with annuals,other
## Larrea flowers without annuals,flies - Larrea flowers without annuals,other
## Annual flowers in open,other - Annual flowers under Ambrosia,other
## Annual flowers in open,other - Annual flowers under Larrea,other
## Annual flowers in open,other - Larrea flowers with annuals,other
## Annual flowers in open,other - Larrea flowers without annuals,other
## Annual flowers under Ambrosia,other - Annual flowers under Larrea,other
## Annual flowers under Ambrosia,other - Larrea flowers with annuals,other
## Annual flowers under Ambrosia,other - Larrea flowers without annuals,other
## Annual flowers under Larrea,other - Larrea flowers with annuals,other
## Annual flowers under Larrea,other - Larrea flowers without annuals,other
## Larrea flowers with annuals,other - Larrea flowers without annuals,other
## estimate SE df z.ratio p.value
## 0.4012223 0.2639919 NA 1.520 0.9736
## 0.6339065 0.2400664 NA 2.641 0.3424
## -26.6912939 3.5029549 NA -7.620 <.0001
## -24.0061349 2.9575033 NA -8.117 <.0001
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## 0.2326842 0.2073677 NA 1.122 0.9987
## -27.0925162 3.5002663 NA -7.740 <.0001
## -24.4073572 2.9473509 NA -8.281 <.0001
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## -27.3252005 3.4988141 NA -7.810 <.0001
## -24.6400414 2.9457096 NA -8.365 <.0001
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## 2.6851590 4.5482332 NA 0.590 1.0000
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## 0.4012223 0.2639919 NA 1.520 0.9736
## 0.6339065 0.2400664 NA 2.641 0.3424
## -26.6912939 3.5029549 NA -7.620 <.0001
## -24.0061349 2.9575033 NA -8.117 <.0001
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## 0.2326842 0.2073677 NA 1.122 0.9987
## -27.0925162 3.5002663 NA -7.740 <.0001
## -24.4073572 2.9473509 NA -8.281 <.0001
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## -27.3252005 3.4988141 NA -7.810 <.0001
## -24.6400414 2.9457096 NA -8.365 <.0001
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## 2.6851590 4.5482332 NA 0.590 1.0000
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## 0.4012223 0.2639919 NA 1.520 0.9736
## 0.6339065 0.2400664 NA 2.641 0.3424
## -26.6912939 3.5029549 NA -7.620 <.0001
## -24.0061349 2.9575033 NA -8.117 <.0001
## 0.2326842 0.2073677 NA 1.122 0.9987
## -27.0925162 3.5002663 NA -7.740 <.0001
## -24.4073572 2.9473509 NA -8.281 <.0001
## -27.3252005 3.4988141 NA -7.810 <.0001
## -24.6400414 2.9457096 NA -8.365 <.0001
## 2.6851590 4.5482332 NA 0.590 1.0000
##
## Results are averaged over the levels of: rep
## P value adjustment: tukey method for comparing a family of 15 estimates#duration of visits
m <- glm(net.visitation~net.treatment + insect.RTU %in% rep + mean.temp, family = "gaussian", data = freq.2015)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: gaussian, link: identity
##
## Response: net.visitation
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 260 4.1594
## net.treatment 3 0.70326 257 3.4561 7.675e-12 ***
## mean.temp 1 0.01179 256 3.4443 0.33800
## insect.RTU:rep 11 0.29868 245 3.1457 0.01623 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1b5 <- AIC(m)
lsmeans(m, pairwise~net.treatment:insect.RTU, adjust="tukey")## $lsmeans
## net.treatment insect.RTU lsmean SE df
## Annual flowers in open bees 0.125038845 0.02021514 NA
## Annual flowers under Larrea bees 0.138510617 0.01688578 NA
## Larrea flowers with annuals bees 0.028977278 0.01764619 NA
## Larrea flowers without annuals bees 0.024828524 0.01746086 NA
## Annual flowers in open flies 0.097162464 0.02102823 NA
## Annual flowers under Larrea flies 0.110634237 0.01825489 NA
## Larrea flowers with annuals flies 0.001100898 0.01876841 NA
## Larrea flowers without annuals flies -0.003047856 0.01843148 NA
## Annual flowers in open other 0.054409949 0.02263407 NA
## Annual flowers under Larrea other 0.067881721 0.01997540 NA
## Larrea flowers with annuals other -0.041651618 0.02207114 NA
## Larrea flowers without annuals other -0.045800372 0.02274373 NA
## asymp.LCL asymp.UCL
## 0.085417905 0.164659785
## 0.105415106 0.171606128
## -0.005608617 0.063563174
## -0.009394131 0.059051179
## 0.055947889 0.138377040
## 0.074855312 0.146413161
## -0.035684501 0.037886297
## -0.039172886 0.033077173
## 0.010047983 0.098771914
## 0.028730656 0.107032786
## -0.084910256 0.001607020
## -0.090377260 -0.001223484
##
## Results are averaged over the levels of: rep
## Results are given on the identity (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast
## Annual flowers in open,bees - Annual flowers under Larrea,bees
## Annual flowers in open,bees - Larrea flowers with annuals,bees
## Annual flowers in open,bees - Larrea flowers without annuals,bees
## Annual flowers in open,bees - Annual flowers in open,flies
## Annual flowers in open,bees - Annual flowers under Larrea,flies
## Annual flowers in open,bees - Larrea flowers with annuals,flies
## Annual flowers in open,bees - Larrea flowers without annuals,flies
## Annual flowers in open,bees - Annual flowers in open,other
## Annual flowers in open,bees - Annual flowers under Larrea,other
## Annual flowers in open,bees - Larrea flowers with annuals,other
## Annual flowers in open,bees - Larrea flowers without annuals,other
## Annual flowers under Larrea,bees - Larrea flowers with annuals,bees
## Annual flowers under Larrea,bees - Larrea flowers without annuals,bees
## Annual flowers under Larrea,bees - Annual flowers in open,flies
## Annual flowers under Larrea,bees - Annual flowers under Larrea,flies
## Annual flowers under Larrea,bees - Larrea flowers with annuals,flies
## Annual flowers under Larrea,bees - Larrea flowers without annuals,flies
## Annual flowers under Larrea,bees - Annual flowers in open,other
## Annual flowers under Larrea,bees - Annual flowers under Larrea,other
## Annual flowers under Larrea,bees - Larrea flowers with annuals,other
## Annual flowers under Larrea,bees - Larrea flowers without annuals,other
## Larrea flowers with annuals,bees - Larrea flowers without annuals,bees
## Larrea flowers with annuals,bees - Annual flowers in open,flies
## Larrea flowers with annuals,bees - Annual flowers under Larrea,flies
## Larrea flowers with annuals,bees - Larrea flowers with annuals,flies
## Larrea flowers with annuals,bees - Larrea flowers without annuals,flies
## Larrea flowers with annuals,bees - Annual flowers in open,other
## Larrea flowers with annuals,bees - Annual flowers under Larrea,other
## Larrea flowers with annuals,bees - Larrea flowers with annuals,other
## Larrea flowers with annuals,bees - Larrea flowers without annuals,other
## Larrea flowers without annuals,bees - Annual flowers in open,flies
## Larrea flowers without annuals,bees - Annual flowers under Larrea,flies
## Larrea flowers without annuals,bees - Larrea flowers with annuals,flies
## Larrea flowers without annuals,bees - Larrea flowers without annuals,flies
## Larrea flowers without annuals,bees - Annual flowers in open,other
## Larrea flowers without annuals,bees - Annual flowers under Larrea,other
## Larrea flowers without annuals,bees - Larrea flowers with annuals,other
## Larrea flowers without annuals,bees - Larrea flowers without annuals,other
## Annual flowers in open,flies - Annual flowers under Larrea,flies
## Annual flowers in open,flies - Larrea flowers with annuals,flies
## Annual flowers in open,flies - Larrea flowers without annuals,flies
## Annual flowers in open,flies - Annual flowers in open,other
## Annual flowers in open,flies - Annual flowers under Larrea,other
## Annual flowers in open,flies - Larrea flowers with annuals,other
## Annual flowers in open,flies - Larrea flowers without annuals,other
## Annual flowers under Larrea,flies - Larrea flowers with annuals,flies
## Annual flowers under Larrea,flies - Larrea flowers without annuals,flies
## Annual flowers under Larrea,flies - Annual flowers in open,other
## Annual flowers under Larrea,flies - Annual flowers under Larrea,other
## Annual flowers under Larrea,flies - Larrea flowers with annuals,other
## Annual flowers under Larrea,flies - Larrea flowers without annuals,other
## Larrea flowers with annuals,flies - Larrea flowers without annuals,flies
## Larrea flowers with annuals,flies - Annual flowers in open,other
## Larrea flowers with annuals,flies - Annual flowers under Larrea,other
## Larrea flowers with annuals,flies - Larrea flowers with annuals,other
## Larrea flowers with annuals,flies - Larrea flowers without annuals,other
## Larrea flowers without annuals,flies - Annual flowers in open,other
## Larrea flowers without annuals,flies - Annual flowers under Larrea,other
## Larrea flowers without annuals,flies - Larrea flowers with annuals,other
## Larrea flowers without annuals,flies - Larrea flowers without annuals,other
## Annual flowers in open,other - Annual flowers under Larrea,other
## Annual flowers in open,other - Larrea flowers with annuals,other
## Annual flowers in open,other - Larrea flowers without annuals,other
## Annual flowers under Larrea,other - Larrea flowers with annuals,other
## Annual flowers under Larrea,other - Larrea flowers without annuals,other
## Larrea flowers with annuals,other - Larrea flowers without annuals,other
## estimate SE df z.ratio p.value
## -0.013471772 0.02651834 NA -0.508 1.0000
## 0.096061566 0.02765390 NA 3.474 0.0258
## 0.100210321 0.02715878 NA 3.690 0.0121
## 0.027876380 0.01601014 NA 1.741 0.8491
## 0.014404608 0.03121095 NA 0.462 1.0000
## 0.123937947 0.03206856 NA 3.865 0.0062
## 0.128086701 0.03154721 NA 4.060 0.0029
## 0.070628896 0.01917063 NA 3.684 0.0123
## 0.057157124 0.03287815 NA 1.738 0.8505
## 0.166690462 0.03470373 NA 4.803 0.0001
## 0.170839217 0.03484047 NA 4.903 0.0001
## 0.109533339 0.02037509 NA 5.376 <.0001
## 0.113682093 0.02068028 NA 5.497 <.0001
## 0.041348153 0.03074036 NA 1.345 0.9732
## 0.027876380 0.01601014 NA 1.741 0.8491
## 0.137409719 0.02577251 NA 5.332 <.0001
## 0.141558473 0.02589835 NA 5.466 <.0001
## 0.084100668 0.03256528 NA 2.583 0.2895
## 0.070628896 0.01917063 NA 3.684 0.0123
## 0.180162235 0.02906058 NA 6.200 <.0001
## 0.184310989 0.02989474 NA 6.165 <.0001
## 0.004148754 0.02117325 NA 0.196 1.0000
## -0.068185186 0.03183916 NA -2.142 0.5925
## -0.081656958 0.02605217 NA -3.134 0.0745
## 0.027876380 0.01601014 NA 1.741 0.8491
## 0.032025135 0.02643111 NA 1.212 0.9882
## -0.025432670 0.03255999 NA -0.781 0.9998
## -0.038904443 0.02684767 NA -1.449 0.9537
## 0.070628896 0.01917063 NA 3.684 0.0123
## 0.074777650 0.02919705 NA 2.561 0.3021
## -0.072333940 0.03150588 NA -2.296 0.4794
## -0.085805712 0.02640592 NA -3.249 0.0529
## 0.023727626 0.02665818 NA 0.890 0.9992
## 0.027876380 0.01601014 NA 1.741 0.8491
## -0.029581425 0.03156527 NA -0.937 0.9987
## -0.043053197 0.02639467 NA -1.631 0.8979
## 0.066480142 0.02791363 NA 2.382 0.4185
## 0.070628896 0.01917063 NA 3.684 0.0123
## -0.013471772 0.02651834 NA -0.508 1.0000
## 0.096061566 0.02765390 NA 3.474 0.0258
## 0.100210321 0.02715878 NA 3.690 0.0121
## 0.042752516 0.02009528 NA 2.127 0.6028
## 0.029280744 0.03320698 NA 0.882 0.9993
## 0.138814082 0.03511874 NA 3.953 0.0044
## 0.142962836 0.03533925 NA 4.045 0.0030
## 0.109533339 0.02037509 NA 5.376 <.0001
## 0.113682093 0.02068028 NA 5.497 <.0001
## 0.056224288 0.03333739 NA 1.687 0.8748
## 0.042752516 0.02009528 NA 2.127 0.6028
## 0.152285854 0.02980052 NA 5.110 <.0001
## 0.156434609 0.03071281 NA 5.093 <.0001
## 0.004148754 0.02117325 NA 0.196 1.0000
## -0.053309051 0.03322335 NA -1.605 0.9079
## -0.066780823 0.02738354 NA -2.439 0.3796
## 0.042752516 0.02009528 NA 2.127 0.6028
## 0.046901270 0.02991325 NA 1.568 0.9207
## -0.057457805 0.03215551 NA -1.787 0.8256
## -0.070929577 0.02682746 NA -2.644 0.2551
## 0.038603762 0.02845086 NA 1.357 0.9713
## 0.042752516 0.02009528 NA 2.127 0.6028
## -0.013471772 0.02651834 NA -0.508 1.0000
## 0.096061566 0.02765390 NA 3.474 0.0258
## 0.100210321 0.02715878 NA 3.690 0.0121
## 0.109533339 0.02037509 NA 5.376 <.0001
## 0.113682093 0.02068028 NA 5.497 <.0001
## 0.004148754 0.02117325 NA 0.196 1.0000
##
## Results are averaged over the levels of: rep
## P value adjustment: tukey method for comparing a family of 12 estimatesm <- glm(net.visitation~net.treatment + insect.RTU %in% rep, family = "gaussian", data = freq.2016)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: gaussian, link: identity
##
## Response: net.visitation
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 229 5.8264
## net.treatment 4 1.0478 225 4.7786 4.716e-13 ***
## insect.RTU:rep 12 1.2777 213 3.5009 1.114e-11 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1b6 <- AIC(m)
lsmeans(m, pairwise~net.treatment:insect.RTU, adjust="tukey")## $lsmeans
## net.treatment insect.RTU lsmean SE df
## Annual flowers in open bees 0.16952604 0.03021296 NA
## Annual flowers under Ambrosia bees 0.15457042 0.03357802 NA
## Annual flowers under Larrea bees 0.21471655 0.03266229 NA
## Larrea flowers with annuals bees 0.04992338 0.03406552 NA
## Larrea flowers without annuals bees 0.05753596 0.03283570 NA
## Annual flowers in open flies NA NA NA
## Annual flowers under Ambrosia flies NA NA NA
## Annual flowers under Larrea flies NA NA NA
## Larrea flowers with annuals flies NA NA NA
## Larrea flowers without annuals flies NA NA NA
## Annual flowers in open other NA NA NA
## Annual flowers under Ambrosia other NA NA NA
## Annual flowers under Larrea other NA NA NA
## Larrea flowers with annuals other NA NA NA
## Larrea flowers without annuals other NA NA NA
## asymp.LCL asymp.UCL
## 0.110309731 0.2287423
## 0.088758706 0.2203821
## 0.150699638 0.2787335
## -0.016843810 0.1166906
## -0.006820815 0.1218927
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
## NA NA
##
## Results are averaged over the levels of: rep
## Results are given on the identity (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast
## Annual flowers in open,bees - Annual flowers under Ambrosia,bees
## Annual flowers in open,bees - Annual flowers under Larrea,bees
## Annual flowers in open,bees - Larrea flowers with annuals,bees
## Annual flowers in open,bees - Larrea flowers without annuals,bees
## Annual flowers in open,bees - Annual flowers in open,flies
## Annual flowers in open,bees - Annual flowers under Ambrosia,flies
## Annual flowers in open,bees - Annual flowers under Larrea,flies
## Annual flowers in open,bees - Larrea flowers with annuals,flies
## Annual flowers in open,bees - Larrea flowers without annuals,flies
## Annual flowers in open,bees - Annual flowers in open,other
## Annual flowers in open,bees - Annual flowers under Ambrosia,other
## Annual flowers in open,bees - Annual flowers under Larrea,other
## Annual flowers in open,bees - Larrea flowers with annuals,other
## Annual flowers in open,bees - Larrea flowers without annuals,other
## Annual flowers under Ambrosia,bees - Annual flowers under Larrea,bees
## Annual flowers under Ambrosia,bees - Larrea flowers with annuals,bees
## Annual flowers under Ambrosia,bees - Larrea flowers without annuals,bees
## Annual flowers under Ambrosia,bees - Annual flowers in open,flies
## Annual flowers under Ambrosia,bees - Annual flowers under Ambrosia,flies
## Annual flowers under Ambrosia,bees - Annual flowers under Larrea,flies
## Annual flowers under Ambrosia,bees - Larrea flowers with annuals,flies
## Annual flowers under Ambrosia,bees - Larrea flowers without annuals,flies
## Annual flowers under Ambrosia,bees - Annual flowers in open,other
## Annual flowers under Ambrosia,bees - Annual flowers under Ambrosia,other
## Annual flowers under Ambrosia,bees - Annual flowers under Larrea,other
## Annual flowers under Ambrosia,bees - Larrea flowers with annuals,other
## Annual flowers under Ambrosia,bees - Larrea flowers without annuals,other
## Annual flowers under Larrea,bees - Larrea flowers with annuals,bees
## Annual flowers under Larrea,bees - Larrea flowers without annuals,bees
## Annual flowers under Larrea,bees - Annual flowers in open,flies
## Annual flowers under Larrea,bees - Annual flowers under Ambrosia,flies
## Annual flowers under Larrea,bees - Annual flowers under Larrea,flies
## Annual flowers under Larrea,bees - Larrea flowers with annuals,flies
## Annual flowers under Larrea,bees - Larrea flowers without annuals,flies
## Annual flowers under Larrea,bees - Annual flowers in open,other
## Annual flowers under Larrea,bees - Annual flowers under Ambrosia,other
## Annual flowers under Larrea,bees - Annual flowers under Larrea,other
## Annual flowers under Larrea,bees - Larrea flowers with annuals,other
## Annual flowers under Larrea,bees - Larrea flowers without annuals,other
## Larrea flowers with annuals,bees - Larrea flowers without annuals,bees
## Larrea flowers with annuals,bees - Annual flowers in open,flies
## Larrea flowers with annuals,bees - Annual flowers under Ambrosia,flies
## Larrea flowers with annuals,bees - Annual flowers under Larrea,flies
## Larrea flowers with annuals,bees - Larrea flowers with annuals,flies
## Larrea flowers with annuals,bees - Larrea flowers without annuals,flies
## Larrea flowers with annuals,bees - Annual flowers in open,other
## Larrea flowers with annuals,bees - Annual flowers under Ambrosia,other
## Larrea flowers with annuals,bees - Annual flowers under Larrea,other
## Larrea flowers with annuals,bees - Larrea flowers with annuals,other
## Larrea flowers with annuals,bees - Larrea flowers without annuals,other
## Larrea flowers without annuals,bees - Annual flowers in open,flies
## Larrea flowers without annuals,bees - Annual flowers under Ambrosia,flies
## Larrea flowers without annuals,bees - Annual flowers under Larrea,flies
## Larrea flowers without annuals,bees - Larrea flowers with annuals,flies
## Larrea flowers without annuals,bees - Larrea flowers without annuals,flies
## Larrea flowers without annuals,bees - Annual flowers in open,other
## Larrea flowers without annuals,bees - Annual flowers under Ambrosia,other
## Larrea flowers without annuals,bees - Annual flowers under Larrea,other
## Larrea flowers without annuals,bees - Larrea flowers with annuals,other
## Larrea flowers without annuals,bees - Larrea flowers without annuals,other
## Annual flowers in open,flies - Annual flowers under Ambrosia,flies
## Annual flowers in open,flies - Annual flowers under Larrea,flies
## Annual flowers in open,flies - Larrea flowers with annuals,flies
## Annual flowers in open,flies - Larrea flowers without annuals,flies
## Annual flowers in open,flies - Annual flowers in open,other
## Annual flowers in open,flies - Annual flowers under Ambrosia,other
## Annual flowers in open,flies - Annual flowers under Larrea,other
## Annual flowers in open,flies - Larrea flowers with annuals,other
## Annual flowers in open,flies - Larrea flowers without annuals,other
## Annual flowers under Ambrosia,flies - Annual flowers under Larrea,flies
## Annual flowers under Ambrosia,flies - Larrea flowers with annuals,flies
## Annual flowers under Ambrosia,flies - Larrea flowers without annuals,flies
## Annual flowers under Ambrosia,flies - Annual flowers in open,other
## Annual flowers under Ambrosia,flies - Annual flowers under Ambrosia,other
## Annual flowers under Ambrosia,flies - Annual flowers under Larrea,other
## Annual flowers under Ambrosia,flies - Larrea flowers with annuals,other
## Annual flowers under Ambrosia,flies - Larrea flowers without annuals,other
## Annual flowers under Larrea,flies - Larrea flowers with annuals,flies
## Annual flowers under Larrea,flies - Larrea flowers without annuals,flies
## Annual flowers under Larrea,flies - Annual flowers in open,other
## Annual flowers under Larrea,flies - Annual flowers under Ambrosia,other
## Annual flowers under Larrea,flies - Annual flowers under Larrea,other
## Annual flowers under Larrea,flies - Larrea flowers with annuals,other
## Annual flowers under Larrea,flies - Larrea flowers without annuals,other
## Larrea flowers with annuals,flies - Larrea flowers without annuals,flies
## Larrea flowers with annuals,flies - Annual flowers in open,other
## Larrea flowers with annuals,flies - Annual flowers under Ambrosia,other
## Larrea flowers with annuals,flies - Annual flowers under Larrea,other
## Larrea flowers with annuals,flies - Larrea flowers with annuals,other
## Larrea flowers with annuals,flies - Larrea flowers without annuals,other
## Larrea flowers without annuals,flies - Annual flowers in open,other
## Larrea flowers without annuals,flies - Annual flowers under Ambrosia,other
## Larrea flowers without annuals,flies - Annual flowers under Larrea,other
## Larrea flowers without annuals,flies - Larrea flowers with annuals,other
## Larrea flowers without annuals,flies - Larrea flowers without annuals,other
## Annual flowers in open,other - Annual flowers under Ambrosia,other
## Annual flowers in open,other - Annual flowers under Larrea,other
## Annual flowers in open,other - Larrea flowers with annuals,other
## Annual flowers in open,other - Larrea flowers without annuals,other
## Annual flowers under Ambrosia,other - Annual flowers under Larrea,other
## Annual flowers under Ambrosia,other - Larrea flowers with annuals,other
## Annual flowers under Ambrosia,other - Larrea flowers without annuals,other
## Annual flowers under Larrea,other - Larrea flowers with annuals,other
## Annual flowers under Larrea,other - Larrea flowers without annuals,other
## Larrea flowers with annuals,other - Larrea flowers without annuals,other
## estimate SE df z.ratio p.value
## 0.014955618 0.02710620 NA 0.552 1.0000
## -0.045190515 0.02587916 NA -1.746 0.9187
## 0.119602658 0.02745821 NA 4.356 0.0013
## 0.111990073 0.02578637 NA 4.343 0.0013
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## -0.060146134 0.02737220 NA -2.197 0.6669
## 0.104647040 0.02888048 NA 3.623 0.0231
## 0.097034455 0.02764675 NA 3.510 0.0340
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## 0.164793173 0.02781487 NA 5.925 <.0001
## 0.157180588 0.02639344 NA 5.955 <.0001
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## -0.007612585 0.02795730 NA -0.272 1.0000
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## 0.014955618 0.02710620 NA 0.552 1.0000
## -0.045190515 0.02587916 NA -1.746 0.9187
## 0.119602658 0.02745821 NA 4.356 0.0013
## 0.111990073 0.02578637 NA 4.343 0.0013
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## -0.060146134 0.02737220 NA -2.197 0.6669
## 0.104647040 0.02888048 NA 3.623 0.0231
## 0.097034455 0.02764675 NA 3.510 0.0340
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## 0.164793173 0.02781487 NA 5.925 <.0001
## 0.157180588 0.02639344 NA 5.955 <.0001
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## -0.007612585 0.02795730 NA -0.272 1.0000
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## NA NA NA NA NA
## 0.014955618 0.02710620 NA 0.552 1.0000
## -0.045190515 0.02587916 NA -1.746 0.9187
## 0.119602658 0.02745821 NA 4.356 0.0013
## 0.111990073 0.02578637 NA 4.343 0.0013
## -0.060146134 0.02737220 NA -2.197 0.6669
## 0.104647040 0.02888048 NA 3.623 0.0231
## 0.097034455 0.02764675 NA 3.510 0.0340
## 0.164793173 0.02781487 NA 5.925 <.0001
## 0.157180588 0.02639344 NA 5.955 <.0001
## -0.007612585 0.02795730 NA -0.272 1.0000
##
## Results are averaged over the levels of: rep
## P value adjustment: tukey method for comparing a family of 15 estimatesAIC contrasts
#Quick interactive-term vs additive-term model comparison
x <- c(a1,a2,a3,a4,a5,a6)
x## [1] -600.2285 -676.8388 -648.3708 -508.2550 -358.2830 -307.5151y <- c(b1,b2,b3,b4,b5,b6)
y## [1] -619.6748 -704.3851 -677.3317 -538.4526 -378.5418 -273.8497z <- abs(x-y)
z## [1] 19.44634 27.54632 28.96084 30.19761 20.25877 33.66544Model: bees only
#Bees####
#visitations
m <- glm(rate.per.flower~net.treatment + mean.temp, family = "Gamma", data = bees.2015)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: Gamma, link: inverse
##
## Response: rate.per.flower
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 119 318.97
## net.treatment 3 160.660 116 158.31 < 2.2e-16 ***
## mean.temp 1 11.944 115 146.37 0.004494 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1require(lsmeans)
lsmeans(m, pairwise~net.treatment, adjust="tukey")## $lsmeans
## net.treatment lsmean SE df asymp.LCL asymp.UCL
## Annual flowers in open 5.039045 1.3045831 NA 2.482110 7.595981
## Annual flowers under Larrea 2.424415 0.5884161 NA 1.271141 3.577689
## Larrea flowers with annuals 40.475520 9.1792372 NA 22.484546 58.466495
## Larrea flowers without annuals 22.581300 5.1274232 NA 12.531736 32.630865
##
## Results are given on the inverse (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate
## Annual flowers in open - Annual flowers under Larrea 2.61463
## Annual flowers in open - Larrea flowers with annuals -35.43648
## Annual flowers in open - Larrea flowers without annuals -17.54226
## Annual flowers under Larrea - Larrea flowers with annuals -38.05111
## Annual flowers under Larrea - Larrea flowers without annuals -20.15689
## Larrea flowers with annuals - Larrea flowers without annuals 17.89422
## SE df z.ratio p.value
## 1.466898 NA 1.782 0.2818
## 9.309342 NA -3.807 0.0008
## 5.326011 NA -3.294 0.0055
## 9.196803 NA -4.137 0.0002
## 5.159868 NA -3.906 0.0005
## 10.510197 NA 1.703 0.3223
##
## P value adjustment: tukey method for comparing a family of 4 estimatesm <- glm(rate.per.flower~net.treatment + mean.temp, family = "Gamma", data = bees.2016)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: Gamma, link: inverse
##
## Response: rate.per.flower
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 106 323.13
## net.treatment 4 278.157 102 44.98 <2e-16 ***
## mean.temp 1 0.331 101 44.65 0.341
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1lsmeans(m, pairwise~net.treatment, adjust="tukey")## $lsmeans
## net.treatment lsmean SE df asymp.LCL
## Annual flowers in open 1.0894275 0.14991960 NA 0.7955905
## Annual flowers under Ambrosia 0.9702642 0.13056940 NA 0.7143529
## Annual flowers under Larrea 0.6750551 0.08492488 NA 0.5086054
## Larrea flowers with annuals 113.3388023 16.61506503 NA 80.7738732
## Larrea flowers without annuals 104.8933091 13.85042846 NA 77.7469682
## asymp.UCL
## 1.3832645
## 1.2261755
## 0.8415048
## 145.9037313
## 132.0396501
##
## Results are given on the inverse (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast
## Annual flowers in open - Annual flowers under Ambrosia
## Annual flowers in open - Annual flowers under Larrea
## Annual flowers in open - Larrea flowers with annuals
## Annual flowers in open - Larrea flowers without annuals
## Annual flowers under Ambrosia - Annual flowers under Larrea
## Annual flowers under Ambrosia - Larrea flowers with annuals
## Annual flowers under Ambrosia - Larrea flowers without annuals
## Annual flowers under Larrea - Larrea flowers with annuals
## Annual flowers under Larrea - Larrea flowers without annuals
## Larrea flowers with annuals - Larrea flowers without annuals
## estimate SE df z.ratio p.value
## 0.1191633 0.1947017 NA 0.612 0.9732
## 0.4143724 0.1639787 NA 2.527 0.0847
## -112.2493747 16.6157093 NA -6.756 <.0001
## -103.8038816 13.8519866 NA -7.494 <.0001
## 0.2952091 0.1548747 NA 1.906 0.3139
## -112.3685381 16.6155749 NA -6.763 <.0001
## -103.9230449 13.8511171 NA -7.503 <.0001
## -112.6637472 16.6152766 NA -6.781 <.0001
## -104.2182540 13.8508157 NA -7.524 <.0001
## 8.4454932 21.6309060 NA 0.390 0.9951
##
## P value adjustment: tukey method for comparing a family of 5 estimatesm <- glm(rate.per.flower.mean.time~net.treatment + mean.temp, family = "Gamma", data = bees.2015)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: Gamma, link: inverse
##
## Response: rate.per.flower.mean.time
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 119 165.621
## net.treatment 3 77.310 116 88.311 < 2.2e-16 ***
## mean.temp 1 11.164 115 77.148 0.0001226 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1lsmeans(m, pairwise~net.treatment, adjust="tukey")## $lsmeans
## net.treatment lsmean SE df asymp.LCL asymp.UCL
## Annual flowers in open 6.538888 1.2131421 NA 4.161173 8.916603
## Annual flowers under Larrea 3.223417 0.5605903 NA 2.124680 4.322154
## Larrea flowers with annuals 13.870940 2.3617363 NA 9.242022 18.499858
## Larrea flowers without annuals 19.032877 3.1062000 NA 12.944837 25.120918
##
## Results are given on the inverse (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate
## Annual flowers in open - Annual flowers under Larrea 3.315471
## Annual flowers in open - Larrea flowers with annuals -7.332051
## Annual flowers in open - Larrea flowers without annuals -12.493989
## Annual flowers under Larrea - Larrea flowers with annuals -10.647523
## Annual flowers under Larrea - Larrea flowers without annuals -15.809460
## Larrea flowers with annuals - Larrea flowers without annuals -5.161938
## SE df z.ratio p.value
## 1.374501 NA 2.412 0.0748
## 2.749456 NA -2.667 0.0384
## 3.368956 NA -3.709 0.0012
## 2.423264 NA -4.394 0.0001
## 3.154964 NA -5.011 <.0001
## 3.896425 NA -1.325 0.5470
##
## P value adjustment: tukey method for comparing a family of 4 estimatesm <- glm(rate.per.flower.mean.time~net.treatment + mean.temp, family = "Gamma", data = bees.2016)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: Gamma, link: inverse
##
## Response: rate.per.flower.mean.time
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 106 201.995
## net.treatment 4 156.925 102 45.070 < 2e-16 ***
## mean.temp 1 1.325 101 43.744 0.05169 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1lsmeans(m, pairwise~net.treatment, adjust="tukey")## $lsmeans
## net.treatment lsmean SE df asymp.LCL
## Annual flowers in open 1.5187631 0.1983433 NA 1.1300172
## Annual flowers under Ambrosia 1.2245303 0.1592723 NA 0.9123623
## Annual flowers under Larrea 0.9146816 0.1112217 NA 0.6966911
## Larrea flowers with annuals 28.3487495 4.0658676 NA 20.3797955
## Larrea flowers without annuals 25.9659706 3.3925913 NA 19.3166138
## asymp.UCL
## 1.907509
## 1.536698
## 1.132672
## 36.317703
## 32.615327
##
## Results are given on the inverse (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast
## Annual flowers in open - Annual flowers under Ambrosia
## Annual flowers in open - Annual flowers under Larrea
## Annual flowers in open - Larrea flowers with annuals
## Annual flowers in open - Larrea flowers without annuals
## Annual flowers under Ambrosia - Annual flowers under Larrea
## Annual flowers under Ambrosia - Larrea flowers with annuals
## Annual flowers under Ambrosia - Larrea flowers without annuals
## Annual flowers under Larrea - Larrea flowers with annuals
## Annual flowers under Larrea - Larrea flowers without annuals
## Larrea flowers with annuals - Larrea flowers without annuals
## estimate SE df z.ratio p.value
## 0.2942328 0.2422478 NA 1.215 0.7429
## 0.6040815 0.2090410 NA 2.890 0.0315
## -26.8299864 4.0704225 NA -6.591 <.0001
## -24.4472076 3.4042025 NA -7.181 <.0001
## 0.3098487 0.1906183 NA 1.625 0.4809
## -27.1242192 4.0689369 NA -6.666 <.0001
## -24.7414404 3.3973478 NA -7.283 <.0001
## -27.4340679 4.0673233 NA -6.745 <.0001
## -25.0512890 3.3957712 NA -7.377 <.0001
## 2.3827788 5.2956187 NA 0.450 0.9915
##
## P value adjustment: tukey method for comparing a family of 5 estimates#duration of visits
m <- glm(net.visitation~net.treatment + mean.temp, family = "gaussian", data = bees.2015)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: gaussian, link: identity
##
## Response: net.visitation
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 119 2.2387
## net.treatment 3 0.70902 116 1.5297 1.43e-11 ***
## mean.temp 1 0.00580 115 1.5239 0.5082
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1lsmeans(m, pairwise~net.treatment, adjust="tukey")## $lsmeans
## net.treatment lsmean SE df asymp.LCL
## Annual flowers in open 0.163020277 0.02977430 NA 0.10466371
## Annual flowers under Larrea 0.137128704 0.02169152 NA 0.09461410
## Larrea flowers with annuals 0.007623393 0.02229334 NA -0.03607075
## Larrea flowers without annuals 0.008081420 0.02180742 NA -0.03466034
## asymp.UCL
## 0.22137684
## 0.17964330
## 0.05131753
## 0.05082318
##
## Results are given on the identity (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast
## Annual flowers in open - Annual flowers under Larrea
## Annual flowers in open - Larrea flowers with annuals
## Annual flowers in open - Larrea flowers without annuals
## Annual flowers under Larrea - Larrea flowers with annuals
## Annual flowers under Larrea - Larrea flowers without annuals
## Larrea flowers with annuals - Larrea flowers without annuals
## estimate SE df z.ratio p.value
## 0.0258915733 0.04036154 NA 0.641 0.9185
## 0.1553968843 0.04113051 NA 3.778 0.0009
## 0.1549388574 0.04004086 NA 3.870 0.0006
## 0.1295053110 0.02949452 NA 4.391 0.0001
## 0.1290472841 0.02949097 NA 4.376 0.0001
## -0.0004580269 0.02976621 NA -0.015 1.0000
##
## P value adjustment: tukey method for comparing a family of 4 estimatesm <- glm(net.visitation~net.treatment, family = "gaussian", data = bees.2016)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: gaussian, link: identity
##
## Response: net.visitation
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 106 4.2059
## net.treatment 4 1.7488 102 2.4571 6.429e-15 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1lsmeans(m, pairwise~net.treatment, adjust="tukey")## $lsmeans
## net.treatment lsmean SE df asymp.LCL
## Annual flowers in open 0.23737179 0.03043881 NA 0.17771282
## Annual flowers under Ambrosia 0.18733333 0.03470559 NA 0.11931164
## Annual flowers under Larrea 0.34730676 0.03236313 NA 0.28387620
## Larrea flowers with annuals 0.01070261 0.03764349 NA -0.06307728
## Larrea flowers without annuals 0.02019841 0.03386918 NA -0.04618397
## asymp.UCL
## 0.29703077
## 0.25535503
## 0.41073732
## 0.08448250
## 0.08658079
##
## Results are given on the identity (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast
## Annual flowers in open - Annual flowers under Ambrosia
## Annual flowers in open - Annual flowers under Larrea
## Annual flowers in open - Larrea flowers with annuals
## Annual flowers in open - Larrea flowers without annuals
## Annual flowers under Ambrosia - Annual flowers under Larrea
## Annual flowers under Ambrosia - Larrea flowers with annuals
## Annual flowers under Ambrosia - Larrea flowers without annuals
## Annual flowers under Larrea - Larrea flowers with annuals
## Annual flowers under Larrea - Larrea flowers without annuals
## Larrea flowers with annuals - Larrea flowers without annuals
## estimate SE df z.ratio p.value
## 0.050038462 0.04616274 NA 1.084 0.8149
## -0.109934968 0.04442852 NA -2.474 0.0964
## 0.226669180 0.04841027 NA 4.682 <.0001
## 0.217173382 0.04553727 NA 4.769 <.0001
## -0.159973430 0.04745366 NA -3.371 0.0067
## 0.176630719 0.05120069 NA 3.450 0.0051
## 0.167134921 0.04849329 NA 3.447 0.0051
## 0.336604149 0.04964277 NA 6.781 <.0001
## 0.327108351 0.04684542 NA 6.983 <.0001
## -0.009495798 0.05063748 NA -0.188 0.9997
##
## P value adjustment: tukey method for comparing a family of 5 estimatesModels: covariates
#Temp####
#Main models capture global effects for temp so need post hoc regressions
#mean temp
#error temp
#CV temp
#Check if cooler under shrubs
#Floral density####
#not captured in global models so need to do here on count and visitation durationsModel: single-magnet hypothesis bees
#Single-magnet hypothesis for bees (drop Larrea flowers)####
#visitations
m <- glm(rate.per.flower~net.treatment + mean.temp, family = "Gamma", data = magnet.bees.2015)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: Gamma, link: inverse
##
## Response: rate.per.flower
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 59 83.419
## net.treatment 1 1.5331 58 81.886 0.2228637
## mean.temp 1 12.5040 57 69.382 0.0004991 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1require(lsmeans)
lsmeans(m, pairwise~net.treatment, adjust="tukey")## $lsmeans
## net.treatment lsmean SE df asymp.LCL asymp.UCL
## Annual flowers in open 4.339556 0.8924756 NA 2.5903356 6.088776
## Annual flowers under Larrea 1.613520 0.5525670 NA 0.5305084 2.696531
##
## Results are given on the inverse (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df
## Annual flowers in open - Annual flowers under Larrea 2.726036 1.237694 NA
## z.ratio p.value
## 2.203 0.0276m <- glm(rate.per.flower~net.treatment + mean.temp, family = "Gamma", data = magnet.bees.2016)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: Gamma, link: inverse
##
## Response: rate.per.flower
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 68 36.148
## net.treatment 2 2.54558 66 33.603 0.02876 *
## mean.temp 1 0.32728 65 33.275 0.33944
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1lsmeans(m, pairwise~net.treatment, adjust="tukey")## $lsmeans
## net.treatment lsmean SE df asymp.LCL asymp.UCL
## Annual flowers in open 1.0579548 0.13119075 NA 0.8008256 1.3150839
## Annual flowers under Ambrosia 0.9392697 0.13130747 NA 0.6819118 1.1966276
## Annual flowers under Larrea 0.6440226 0.08462058 NA 0.4781693 0.8098758
##
## Results are given on the inverse (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate
## Annual flowers in open - Annual flowers under Ambrosia 0.1186850
## Annual flowers in open - Annual flowers under Larrea 0.4139322
## Annual flowers under Ambrosia - Annual flowers under Larrea 0.2952472
## SE df z.ratio p.value
## 0.1928844 NA 0.615 0.8117
## 0.1624461 NA 2.548 0.0292
## 0.1534445 NA 1.924 0.1319
##
## P value adjustment: tukey method for comparing a family of 3 estimatesm <- glm(rate.per.flower.mean.time~net.treatment + mean.temp, family = "Gamma", data = magnet.bees.2015)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: Gamma, link: inverse
##
## Response: rate.per.flower.mean.time
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 59 62.284
## net.treatment 1 1.3676 58 60.917 0.201220
## mean.temp 1 11.6685 57 49.248 0.000189 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1lsmeans(m, pairwise~net.treatment, adjust="tukey")## $lsmeans
## net.treatment lsmean SE df asymp.LCL asymp.UCL
## Annual flowers in open 5.714829 1.0675878 NA 3.6223951 7.807262
## Annual flowers under Larrea 2.164790 0.6648291 NA 0.8617487 3.467831
##
## Results are given on the inverse (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df
## Annual flowers in open - Annual flowers under Larrea 3.550039 1.485907 NA
## z.ratio p.value
## 2.389 0.0169m <- glm(rate.per.flower.mean.time~net.treatment + mean.temp, family = "Gamma", data = magnet.bees.2016)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: Gamma, link: inverse
##
## Response: rate.per.flower.mean.time
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 68 35.764
## net.treatment 2 2.0697 66 33.695 0.04584 *
## mean.temp 1 1.2838 65 32.411 0.05052 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1lsmeans(m, pairwise~net.treatment, adjust="tukey")## $lsmeans
## net.treatment lsmean SE df asymp.LCL asymp.UCL
## Annual flowers in open 1.4330433 0.1685832 NA 1.1026263 1.763460
## Annual flowers under Ambrosia 1.1421732 0.1558070 NA 0.8367971 1.447549
## Annual flowers under Larrea 0.8320886 0.1056443 NA 0.6250295 1.039148
##
## Results are given on the inverse (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate
## Annual flowers in open - Annual flowers under Ambrosia 0.2908702
## Annual flowers in open - Annual flowers under Larrea 0.6009548
## Annual flowers under Ambrosia - Annual flowers under Larrea 0.3100846
## SE df z.ratio p.value
## 0.2372098 NA 1.226 0.4376
## 0.2046763 NA 2.936 0.0093
## 0.1867141 NA 1.661 0.2205
##
## P value adjustment: tukey method for comparing a family of 3 estimates#duration of visits
m <- glm(net.visitation~net.treatment + mean.temp, family = "gaussian", data = magnet.bees.2015)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: gaussian, link: identity
##
## Response: net.visitation
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 59 1.5512
## net.treatment 1 0.028938 58 1.5223 0.2952
## mean.temp 1 0.017059 57 1.5052 0.4215lsmeans(m, pairwise~net.treatment, adjust="tukey")## $lsmeans
## net.treatment lsmean SE df asymp.LCL asymp.UCL
## Annual flowers in open 0.1494341 0.04543425 NA 0.06038457 0.2384836
## Annual flowers under Larrea 0.1583251 0.04314468 NA 0.07376309 0.2428871
##
## Results are given on the identity (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate
## Annual flowers in open - Annual flowers under Larrea -0.008891048
## SE df z.ratio p.value
## 0.07800147 NA -0.114 0.9092m <- glm(net.visitation~net.treatment, family = "gaussian", data = magnet.bees.2016)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: gaussian, link: identity
##
## Response: net.visitation
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 68 2.7353
## net.treatment 2 0.29422 66 2.4411 0.01873 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1lsmeans(m, pairwise~net.treatment, adjust="tukey")## $lsmeans
## net.treatment lsmean SE df asymp.LCL asymp.UCL
## Annual flowers in open 0.2373718 0.03771687 NA 0.1634481 0.3112955
## Annual flowers under Ambrosia 0.1873333 0.04300384 NA 0.1030473 0.2716193
## Annual flowers under Larrea 0.3473068 0.04010129 NA 0.2687097 0.4259038
##
## Results are given on the identity (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate
## Annual flowers in open - Annual flowers under Ambrosia 0.05003846
## Annual flowers in open - Annual flowers under Larrea -0.10993497
## Annual flowers under Ambrosia - Annual flowers under Larrea -0.15997343
## SE df z.ratio p.value
## 0.05720046 NA 0.875 0.6562
## 0.05505157 NA -1.997 0.1129
## 0.05880004 NA -2.721 0.0179
##
## P value adjustment: tukey method for comparing a family of 3 estimatesModel: double-magnet hypothesis bees
#Single-magnet hypothesis for bees (drop Larrea flowers)####
#visitations
m <- glm(rate.per.flower~net.treatment + mean.temp, family = "Gamma", data = double.bees.2015)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: Gamma, link: inverse
##
## Response: rate.per.flower
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 59 81.399
## net.treatment 1 4.9722 58 76.427 0.1064
## mean.temp 1 0.1861 57 76.241 0.7548require(lsmeans)
lsmeans(m, pairwise~net.treatment, adjust="tukey")## $lsmeans
## net.treatment lsmean SE df asymp.LCL asymp.UCL
## Larrea flowers with annuals 41.45462 10.430013 NA 21.01217 61.89707
## Larrea flowers without annuals 23.17447 5.841919 NA 11.72452 34.62442
##
## Results are given on the inverse (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate
## Larrea flowers with annuals - Larrea flowers without annuals 18.28016
## SE df z.ratio p.value
## 11.9334 NA 1.532 0.1256m <- glm(rate.per.flower~net.treatment + mean.temp, family = "Gamma", data = double.bees.2016)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: Gamma, link: inverse
##
## Response: rate.per.flower
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 37 11.430
## net.treatment 1 0.05464 36 11.375 0.6978
## mean.temp 1 0.49572 35 10.879 0.2421lsmeans(m, pairwise~net.treatment, adjust="tukey")## $lsmeans
## net.treatment lsmean SE df asymp.LCL asymp.UCL
## Larrea flowers with annuals 130.65268 23.19997 NA 85.18157 176.1238
## Larrea flowers without annuals 93.59244 16.31078 NA 61.62391 125.5610
##
## Results are given on the inverse (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate
## Larrea flowers with annuals - Larrea flowers without annuals 37.06023
## SE df z.ratio p.value
## 33.07033 NA 1.121 0.2624m <- glm(rate.per.flower.mean.time~net.treatment + mean.temp, family = "Gamma", data = double.bees.2015)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: Gamma, link: inverse
##
## Response: rate.per.flower.mean.time
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 59 28.567
## net.treatment 1 1.17239 58 27.395 0.1862
## mean.temp 1 0.00874 57 27.386 0.9091lsmeans(m, pairwise~net.treatment, adjust="tukey")## $lsmeans
## net.treatment lsmean SE df asymp.LCL asymp.UCL
## Larrea flowers with annuals 14.85401 2.225340 NA 10.49243 19.21560
## Larrea flowers without annuals 19.68867 2.947441 NA 13.91180 25.46555
##
## Results are given on the inverse (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate
## Larrea flowers with annuals - Larrea flowers without annuals -4.834661
## SE df z.ratio p.value
## 3.697885 NA -1.307 0.1911m <- glm(rate.per.flower.mean.time~net.treatment + mean.temp, family = "Gamma", data = double.bees.2016)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: Gamma, link: inverse
##
## Response: rate.per.flower.mean.time
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 37 11.430
## net.treatment 1 0.05464 36 11.375 0.6978
## mean.temp 1 0.49572 35 10.879 0.2421lsmeans(m, pairwise~net.treatment, adjust="tukey")## $lsmeans
## net.treatment lsmean SE df asymp.LCL asymp.UCL
## Larrea flowers with annuals 32.66317 5.799992 NA 21.29539 44.03095
## Larrea flowers without annuals 23.39811 4.077694 NA 15.40598 31.39024
##
## Results are given on the inverse (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate
## Larrea flowers with annuals - Larrea flowers without annuals 9.265059
## SE df z.ratio p.value
## 8.267581 NA 1.121 0.2624#duration of visits
m <- glm(net.visitation~net.treatment + mean.temp, family = "gaussian", data = double.bees.2015)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: gaussian, link: identity
##
## Response: net.visitation
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 59 0.0074550
## net.treatment 1 3.5012e-05 58 0.0074200 0.6040
## mean.temp 1 2.0700e-07 57 0.0074198 0.9682lsmeans(m, pairwise~net.treatment, adjust="tukey")## $lsmeans
## net.treatment lsmean SE df asymp.LCL
## Larrea flowers with annuals 0.002699756 0.002085387 NA -0.001387527
## Larrea flowers without annuals 0.004235429 0.002085387 NA 0.000148146
## asymp.UCL
## 0.006787039
## 0.008322712
##
## Results are given on the identity (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate
## Larrea flowers with annuals - Larrea flowers without annuals -0.001535673
## SE df z.ratio p.value
## 0.002952495 NA -0.52 0.6030m <- glm(net.visitation~net.treatment, family = "gaussian", data = double.bees.2016)
anova(m, test = "Chisq")## Analysis of Deviance Table
##
## Model: gaussian, link: identity
##
## Response: net.visitation
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL 37 0.016865
## net.treatment 1 0.00084713 36 0.016018 0.1676lsmeans(m, pairwise~net.treatment, adjust="tukey")## $lsmeans
## net.treatment lsmean SE df asymp.LCL
## Larrea flowers with annuals 0.01070261 0.005115991 NA 0.0006754572
## Larrea flowers without annuals 0.02019841 0.004603038 NA 0.0111766243
## asymp.UCL
## 0.02072977
## 0.02922020
##
## Results are given on the identity (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate
## Larrea flowers with annuals - Larrea flowers without annuals -0.009495798
## SE df z.ratio p.value
## 0.006881956 NA -1.38 0.1676Modeling assumptions
- It is acceptable to aggregate all treatments into one vector.
- The best fit model included interaction terms (not additive) and nests insect.RTU within reps. However, contrasts of AIC scores suggest that the additive model was best fit and given data viz and non-orthogonality issues, a compelling argument can be made for an additive global model.
- It is acceptable to treat each year separately and not in a single model (no Ambrosia in 2015 and different years).
- It is acceptable to model only bee data because of data viz.
- The appropriate model is a GLM with fixed effects. This assumes rep is fixed and not random effect in single-year models. A multi-year model would be modeled using glmer or glmer.nb because year would be treated as random.
- Gamma is the most likely family in several instances. Tests with weibull and others did not change outcome.
- The function lsmeans is the most appropriate for posthoc contrasts (main model has a nested effect). This is not always ideal. The function glht etc from multcomp package was also tested and performed similarly. The function lsmeansLT from lmerTest package if there is a random effect in model (and mixed) was similar and difflsmeans as well. The final option is to do a likelihood ratio post hoc tests with a chi-sq approximation (following main glmer fit). This involves fitting model then repeating with a null, intercept-only model and comparing the two fits.
Interpretation
- Cannot ignore taxa specificity. Data viz clearly shows that bees were the only taxa to respond to treatments (and that by plotting without taxa this is lost).
- Larrea flowers are not as attractive to bees as annuals within this ecosystem.
- Bees repond to temp.
- There is support for the single-magnet hypothesis.
- Both shrub species can generally facilitate annuals through pollination.
- There is no support for the double-magnet prediction, i.e. shrubs receive no reciprocal benefit or facilitation from annuals.
- Bees are the most effective pollinators, i.e. they also spend the most time with flowers and likely are the most effective service pollinators.
Supporting analyses
#test multiple vector data structure####
#test Rii####